Biology1010, Michael T. Stevens
Invitation to Biology
Chapter 1
What is Science?

The Scientific World View
1) By working together over time, people can figure out how the world works.
2) The universe is a unified system and knowledge gained from studying one part of it can often be applied to other parts.
3) Knowledge is both stable and subject to change.
from Benchmarks for Science Literacy

Why am I taking this class?
When people know how scientists work and reach scientific conclusions, and what the limitations of such conclusions are, they are more likely to react thoughtfully to scientific claims and less likely to reject them out of hand or accept them uncritically
from Benchmarks for Science Literacy

Why am I taking this class?
Once people gain a good sense of how science operates—along with a basic inventory of key science concepts as a basis for learning more later—they can follow the science adventure story as it plays out during their lifetimes.
from Benchmarks for Science Literacy

1.5 &1.6 How science operates: The nature of scientific Inquiry
More flexible than a rigid set of steps “the scientific method.”
Can involve:
Making observations
Asking questions
Gathering information
Collecting and analyzing data
Making conclusions and sharing results

Scientific Theory
A widely accepted hypothesis that has been repeatedly tested and never refuted
Theories have wide-ranging explanatory power

Examples of Scientific Theories
Theory of Evolution by Natural Selection
The Cell Theory
Atomic Theory
The Theory of Continental Drift
The Heliocentric Theory

Limits of Science
Scientific inquiry does not address:
subjective questions
the supernatural

1.7 Role of Experiments
Procedures used to study a phenomenon under known conditions
Allows you to test a hypothesis
Hypotheses are supported or refuted with evidence, they are not proved true or false.

Experimental Design
Experimental group
A group exposed to the variable of interest
Control group
A standard for comparison
Identical to experimental group except for variable being studied

Things to consider:

Sampling error
Non-representative sample skews results
Minimize by:
Using large sample sizes

More biased
Privately-funded research
Work done by one individual

Less biased
Government-funded research (NSF)
Interdisciplinary or Collaborative Work

Scientists make observations
Scientists ask questions
Why do certain aspen trees get eaten by caterpillars while others do not?
Do the aspen trees that get eaten grow less than the aspen that don’t get eaten?
Scientists gather information about the things they plan to study
Quaking aspen (Populus tremuloides)
Herbivores—animals that eat plants
-forest tent caterpillar
-large aspen tortrix
-gypsy moth caterpillar
Chemicals in aspen leaves
Phenolic glycosides
A caterpillar’s taste test
Scientists predict what will happen in their experiments
Different aspen trees have different amounts of chemicals that taste bad to caterpillars.
Aspen trees that don’t get eaten by caterpillars grow more than aspen that do get eaten.
Scientists do experiments
Variables in the experiment
Genotype—each aspen tree has different genes
Defoliation—some trees had their leaves removed, others didn’t
Scientists collect data
Measured chemicals
Measured tree growth
Scientists analyze data
Leaf chemicals
Scientists draw conclusions
Aspen trees have different amounts of leaf chemicals. (Genetic variation in leaf chemistry)
The amount of leaf chemicals are affected by whether or not the tree got eaten. (Induction)
Trees that get eaten grow less. (Negative effects of defoliation)
Over time, trees with more leaf chemicals will grow faster and make more seeds than their neighbors
These seeds grow into new trees
So, the next generation of trees will have more leaf chemicals
Aspen Population
Green = taste good (few chemicals)
Red = taste bad (many chemicals)
Changes in populations over time
How species (like trees and caterpillars) work together in their environment
Scientists share their results

1.1 Life’s Levels of Organization
The cell is the basic unit of life
Living things show levels of organization, from the simple to the complex
Cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, the biosphere
Cells are composed of the molecules of life

Nucleic acids (DNA and RNA)
Proteins (muscles)
Carbohydrates (sugars and starch)
Lipids (fats)

1.2 Life’s Unity DNA (deoxyribonucleic acid)
The signature molecule of life
Molecule of inheritance
Directs assembly of amino acids into proteins
Heritability of DNA
DNA is transmitted from parent to offspring via reproduction
DNA codes for traits and directs the development of an organism

Energy Is the Basis of Metabolism
Energy = Capacity to do work
Metabolism = Reactions by which cells acquire and use energy to grow, survive, and reproduce
Interdependencies among Organisms

Make their own food
Depend on energy stored in tissues of producers or other consumers

Energy Flow
Usually starts with energy from sun
Transferred from one organism to another
Energy flows in one direction
Eventually all energy dissipates as heat

Life responds to change
Organisms sense changes in their environment and make responses to them
Receptors detect specific forms of energy
The form of energy detected by a receptor is a stimulus
Maintenance of internal environment within range suitable for cell activities

Unity of Life Overview
All organisms:
Are composed of the same substances
Engage in metabolism
Sense and respond to the environment
Have the capacity to reproduce based on instructions in DNA

1.3 Diversity of Life
Millions of living species
Additional millions of species now extinct
Classification scheme attempts to organize this diversity

No nucleus
No organelles
Ex: bacteria

DNA is inside a nucleus
Have organelles
Most are larger and more complex than the prokaryotes
Can be unicellular or multicellular

Three-Domain Classification
Eukarya (Eukaryotes)—protists, plants, fungi, and animals

Some unicellular, some multicellular
Can be producers or consumers
Challenging group to classify
Ex: paramecia, amoebas, algae

Almost all are multicellular
Most are photosynthetic producers
Make up the food base for communities
Ex: aspen, pines, wheat

Most are multicellular
Consumers and decomposers
Extracellular digestion and absorption
Ex: mushrooms, yeasts, molds

Multicellular consumers
Move about during at least some stage of their life

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
Scientific Names
Two-part naming system devised by Carolus Linnaeus
First name is genus (plural, genera)
Second name is species
Homo sapiens
Populus tremuloides

Chapter 2: Life’s chemical basis
2.1 Atom—smallest unit that retains the properties of an element.
Proton—positive charge, in nucleus
Neutron—no charge, in nucleus
Electron—negative charge, orbits nucleus
Periodic Table
If you know the number of protons, neutrons, and electrons, you can predict the behavior of an element.
Atomic number = number of protons, unique for each element
Mass number = number of protons + number of neutrons
Elements in the same column of the table have the same number of electrons available for interaction.

2.2 Radioisotopes
Isotope—two or more forms of an element that differ in neutron number.
Ex: Hydrogen isotopes: protium, deuterium and tritium
Ex: Carbon isotopes: 12C,13C, and 14C
Isotopes with too many or too few neutrons are often unstable and are radioactive.
Radioisotopes of Carbon
Living things produce different forms of carbon.
Once an organism dies, 14C starts to decay. Half of the 14C decays in 5,700 years.
Used to estimate the age of fossils.
Used as tracers in experiments
Used medicinally

2.3 Electrons and energy levels
Electrons occupy orbitals.
Orbitals closest to the nucleus have the lowest levels of energy.
Electrons fill the lower levels first.
The lowest level can hold two electrons, higher levels hold eight.

Chemical bonding
Atoms give up, acquire, and share electrons with other atoms.
Chemical bonding results in:
Molecules—two or more atoms of the same or different elements joined in a chemical bond

2.4 Atomic Interactions
1) Ionic Bonding
Ion: An atom with a positive or negative charge. Ions form when an atom gains or loses electrons.
Ionic Bond: The close association of charged atoms

2) Covalent Bonding
Covalent Bond: When atoms share one or more electrons.
One pair shared (single bond) H-H
Two pairs shared (double bond) O=O
Three pairs shared (triple bond)
Covalent bonds are more stable and stronger than ionic bonds.

3) Hydrogen bonding: a result of polarity
Nonpolar: electrons shared equally, no poles
Ex: H2, O2, N2
Polar: One atom has a stronger pull on the electrons so the molecule has positive and negative poles.
Ex: H2O

Hydrogen Bonding
An interaction involving hydrogen (+) and some other part of a molecule (-).
Bonds that can form and break easily.
Crucial biological roles in DNA and water.

2.5 Water’s life-giving properties
1) Polarity of water—no net charge, but has a positive (H) and negative (O) end.
Attracts other polar molecules such as sugars and salts (hydrophilic)
Repels oil and other nonpolar molecules (hydrophobic)
Hydrophilic/phobic interactions important for the formation of cell membranes
2) Water is temperature stabilizing
Compared with other fluids, water can absorb a lot of heat energy before increasing in temperature. (High specific heat)
Why?—hydrogen bonding
Evaporation of Water
As water molecules break free, they carry away heat energy
Evaporative water loss is used by mammals to lower body temperature
Why Ice Floats
In ice, hydrogen bonds lock molecules in a lattice
Water molecules in lattice are spaced farther apart then those in liquid water
Ice is less dense than water
Water Is a Good Solvent
Ions and polar molecules dissolve easily in water
When solute dissolves, water molecules cluster around solute molecules and keep them separated
Water Cohesion
Hydrogen bonding holds water molecules together
Creates surface tension
Allows water to move as continuous column upward through stems of plants

2.6 Acids and Bases
H2O splits into ions of hydrogen (H+) and hydroxide (OH-) in equal amounts. Water is neutral.
Acids have more H+ ions.
Bases have fewer H+ ions, they have more OH- ions.
The pH Scale
Measures H+ concentration
Change of 1 on scale means 10X change in H+ concentration

Highest H+ Lowest H+
Acidic Neutral Basic

Examples of pH
Pure water is neutral with pH of 7.0
Stomach acid: pH 1.0 - 3.0
Lemon juice: pH 2.3
Baking soda: pH 9.0
Household ammonia: pH 11.0

Molecules of Life
Chapter 3
3.1 Organic Compounds
Contain carbon and at least one hydrogen atom.
Nucleic Acids

Carbon’s Bonding Behavior
Outer shell of carbon has 4 electrons; can hold 8
Each carbon atom can form covalent bonds with up to four atoms
Bonding Arrangements
Carbon atoms can form chains or rings
Atoms can project from the carbon backbone

Functional Groups
Atoms or clusters of atoms that are covalently bonded to carbon backbone
Give organic compounds their different properties
Examples of Functional Groups
Hydroxyl group - OH
Methyl group -CH3
Carboxyl group - COOH
Amino group - NH3+
Phosphate group - PO3-

How do cells build organic compounds?
With the help of enzymes, cells build polymers from monomers.
Enzyme—a protein that accelerates a reaction
Monomer—small organic compound
Polymer—a molecule that contains repeating monomers

Types of Reactions
Functional group transfer
Electron transfer
Cleavage (Hydrolysis)

Condensation Reactions
Form polymers from subunits
Enzymes remove -OH from one molecule, H from another, form bond between two molecules
The removed –OH and H can join to form water

A type of cleavage reaction
Breaks polymers into smaller units
Enzymes split molecules into two or more parts
An -OH group and an H atom derived from water are attached at exposed sites

3.2 Carbohydrates
The most abundant biological molecules in nature.
Consist of C, H, O in a 1:2:1 ratio.
1) Monosaccharides (simple sugars, one sugar unit)
2) Oligosaccharides (short-chain carbohydrates)
3) Polysaccharides (complex carbohydrates)

Simplest carbohydrates
Most are sweet-tasting, water-soluble
Most have 5- or 6-carbon backbone
Examples: glucose, fructose, ribose, deoxyribose

Two Monosaccharides
Disaccharide = 2 monosaccharides covalently bonded
Formed by condensation reaction

Straight or branched chains of many sugar monomers
Most common are composed entirely of glucose

Cellulose & Starch
Differ in bonding patterns between monomers
Cellulose - tough, indigestible, structural material in plants
Starch - easily digested, storage form in plants

Sugar storage form in animals
Large stores in muscle and liver cells
When blood sugar decreases, liver cells degrade glycogen, release glucose

3.3 Lipids
Nonpolar hydrocarbons
Most include fatty acids
Glycerides (fats and oils)
Phospholipids (cell membranes)
Fatty Acids
Carboxyl group (-COOH) at one end
Carbon backbone (up to 36 C atoms)
Saturated - Single bonds between carbons
Unsaturated - One or more double bonds
Three Fatty Acids
Glycerides (fats and oils)
Glycerol and 3 fatty acids
Butter, lard, vegetable oil.
Yield more than 2X energy/gram than carbs.
Important for storage.
Main components of cell membranes
Hydrophilic heads (polar), hydrophobic tails (nonpolar).
Fatty acids linked to alcohols or carbon rings
Firm consistency, protect, lubricate
Repel water (bird feathers)
Prevent water loss (cuticle on plant leaves)
No fatty acids
Rigid backbone of four fused carbon rings
Cholesterol, Estrogen, Testosterone

3.4 Proteins
Very diverse
Important for structure, nutrition, enzymatic reactions, cell communication.
Made from amino acids
Amino Acids
Amino group
Carboxyl group
R group—20 R groups, one for each different amino acid

Protein Synthesis
Protein is a chain of amino acids l

3.4 Proteins
Very diverse
Important for structure, nutrition, enzymatic reactions, cell communication.
Made from amino acids
Amino Acids
Amino group
Carboxyl group
R group—20 R groups, one for each different amino acid

Protein Synthesis
Protein is a chain of amino acids linked by peptide bonds
Peptide bond
Type of covalent bond
Forms through condensation reaction
Primary Structure
Sequence of amino acids
Unique for each protein
Two linked amino acids = dipeptide
Three or more = polypeptide

Primary Structure & Protein Shape
Primary structure influences protein shape:
H bonding between different amino acids
R group interaction

Secondary Structure
Hydrogen bonds form between different parts of polypeptide chain
These bonds give rise to coils (helices) or pleated sheets
Examples of Secondary Structure

Tertiary Structure
Folding and coiling as a result of interactions between R groups

Quaternary Structure
Some proteins are made up of more than one polypeptide chain

Polypeptides With Attached Organic Compounds
Proteins combined with fats
Proteins combined with sugars

3.5 Importance of Protein Structure
The substitution of one amino acid (valine for glutamate) changes the shape of red blood cells and results in sickle-cell anemia.
Disruption of three-dimensional shape
Breakage of weak bonds
Causes of denaturation:
Destroying protein shape disrupts function
Ex: Cooking an egg

3.6 Nucleotides make up Nucleic Acids
Nucleotide—a small organic compound with:
sugar (deoxyribose or ribose)
base (contains nitrogen)

Nucleic Acid—single- or double-stranded molecule composed of nucleotides (e.g., DNA and RNA).
Consists of four types of nucleotides:
Adenine Thymine Guanine Cytosine
A pairs with T
G pairs with C

Usually single strands
Four types of nucleotides
Adenine pairs with Uracil
Guanine pairs with Cytosine
RNA is a key player in protein synthesis
Nucleotides also function as energy carriers—ATP (adenosine triphosphate)

Cell Structure and Function
Chapter 4

4.1 The Cell
Smallest unit of life
Metabolically active
Senses and responds to environment
Has potential to grow and reproduce
Cell Structure
All have:
Plasma membrane
Region where DNA is stored

Why Are Cells Small?
Surface-to-volume ratio
The bigger a cell is, the less surface area there is per unit volume
Above a certain size, material cannot be moved in or out of cell fast enough
Surface-to-Volume Ratio

4.2 How we see cells
Mid 1600s - Robert Hooke—cork cells
Late 1600s - Antony van Leeuwenhoek—protists, bacteria, sperm cells
1820s - Robert Brown—plant cell nucleus
Developing Cell Theory (mid 1800s)
Matthias Schleiden—plant tissue is composed of cells
Theodor Schwann—animal tissue is composed of cells
Rudolf Virchow—all cells come from other cells

Cell Theory
1) All life is composed of cells
2) Cell is smallest unit having properties of life
3) New cells come from previously existing cells

Light microscopes
Electron microscopes
Transmission EM
Scanning EM
Light Microscopes
Living samples
Natural color
Can resolve objects down to about 200 nm

Electron Microscopy

Uses streams of accelerated electrons rather than lightElectrons are focused by magnets rather than glass lenses
Can resolve structures down to 0.5 nm
Samples are dead
Black-and-white images
Transmission vs. Scanning Electron Microscopes

4.3 Cell Membranes
Main component: a lipid bilayer
Gives the membrane its fluid properties
Two layers of phospholipids

Fluid Mosaic Model
Membrane is a mosaic of

4.4 Prokaryotic Cells
Small and simple, metabolically diverse
DNA is not enclosed in nucleus
No organelles
Ex: Archaea and Eubacteria
Prokaryotic Structure

4.6 Eukaryotic Cells
Larger and more complex cells
DNA is enclosed in a nucleus
Have organelles
Ex: Plants, Animals, Protists, Fungi

4.7 Functions of the Nucleus
Keeps DNA separated from the metabolic machinery of the cytoplasm
Makes it easier to organize and copy DNA before cell divison
Components of the Nucleus

4.8 Components of Endomembrane System
Endoplasmic reticulum
Golgi bodies
Endoplasmic Reticulum
System of membranous channels extending throughout cytoplasm
Lipid synthesis, initial modification of proteins
Two types: smooth and rough
Smooth ER
No ribosomes on surface
Lipid assembly
Rough ER
Ribosomes give it a rough appearance
Initial modification of polypeptides
Golgi Bodies
Consists of slightly curved sacs
Final modification of proteins and lipids
Packaging and sorting for cell use and export
Material arrives and leaves in vesicles
Membranous sacs that move through the cytoplasm, cellular recycling centers
Lysosomes—contain digestive enzymes
Peroxisomes—breakdown hydrogen peroxide and alcohol
Central Vacuole
Only in plants
Many fused vesicles
Fluid-filled organelle
Stores amino acids, sugars, pigments, toxins
Can take up 50-90 percent of cell interior

4.9 Mitochondria
Double-membrane bound organelles
Inner membranes (Cristae) are folded
Sites of respiration—where organic compounds are converted to energy using oxygen.
ATP-producing powerhouses
In plants and animals

4.9 Chloroplasts
Double membrane bound organelles with inner thylakoid membranes
Thylakoids contain chlorophyll
Important for photosynthesis—using light energy to make carbohydrates
Only in plants and protists—not in animals

Endosymbiont Theory
Both mitochondria and chloroplasts resemble prokaryotes in size and structure
Have own DNA, RNA, and ribosomes
Evidence shows that they were free-living and then moved inside larger cells

4.10 Plant Cell Features
Animal Cell Features

4.12 Cytoskeleton
Present in all eukaryotic cells
Basis for cell shape and internal organization
Allows organelle movement within cells and cell motility
Cytoskeletal Elements
Microtubules vs. Microfilaments
Microtubules found in cilia and flagella
Microfilaments are found in pseudopods
Cilia and Flagella
Cilia—short, usually numerous hair-like projections that undulate
Ex: Paramecium, human respiratory tract
Flagella—longer, usually fewer whip-like projections
Ex: Euglena, sperm cells
All eukaryotic cilia and flagella have the same 9 + 2 structure of microtubules—evidence for evolution
Temporary, irregular lobes that project from the cell and function in locomotion and prey capture
Have microfilaments
Ex: Amoeba

How Cells Work
Chapter 5
5.1 What Is Energy?
Capacity to do work
Forms of energy
Motion, chemical energy, heat, electricity, sound, nuclear forces, gravity
First Law of Thermodynamics
The total amount of energy in the universe remains constant
Energy can be converted from one form to another, but it cannot be created or destroyed
Second Law of Thermodynamics
No energy conversion is ever 100 percent efficient
Entropy—a measure of a system’s disorder
Disorder always increases.

One-Way Flow of Energy
Organisms maintain order by being resupplied with energy
The sun is life’s primary energy source
Energy flows in one direction from more usuable to less usable forms
Heat is the least usuable form of energy

Endergonic Reactions
Energy input required
Product has more energy than starting substances
Ex: CO2 + H20 = glucose + O2 (Photosynthesis)

Exergonic Reactions
Energy is released
Products have less energy than starting substance
Ex: glucose + O2 = CO2 + H2O
The role of ATP
Cells use ATP in endergonic reactions
Cells gain ATP in exergonic
Cells couple these two types of reactions
When ATP gives up a phosphate, ADP forms
ATP can re-form when ADP gains a phosphate group (phosphorylation)
This cycle helps drive most metabolic reactions

5.2 & 5.5 Participants in Metabolic Reactions
Reactants—starting substances
Intermediates—substances formed during a reaction sequence
Products—substances left at the end
Chemical Equilibrium

Redox Reactions
Cells release energy through electron transfers
Oxidation-reduction (redox) reactions
One molecule gives up electrons (is oxidized) and another gains them (is reduced)
H+ ions are transferred at the same time

Electron Transfer Chains
Arrangement of enzymes and coenzymes at a cell membrane
As one molecule is oxidized, next is reduced
Important in photosynthesis and aerobic respiration
Uncontrolled vs. Controlled Energy Release

Metabolic Pathways
Enzyme-mediated sequences of reactions in cells
Biosynthetic (anabolic) – ex: photosynthesis
Degradative (catabolic) – ex: aerobic respiration

5.3 Enzymes
Generally proteins
Speed up reactions
Not altered or used up in reactions
Work in forward and reverse reactions
Specific--each type of enzyme recognizes and binds to only certain substrates

Activation Energy
For a reaction to occur, an energy barrier must be surmounted
Enzymes make the energy barrier smaller

5.4 How Enzymes Work
1) Concentrate substrates at the active site
2) Orient the substrates in positions favoring reactions
3) Shut out competing reactions

Factors Influencing Enzyme Activity
Allosteric regulators
Effect of Temperature
Effect of pH
Enzyme Helpers
Cofactors—assist enzymatic reactions by accepting and receiving electrons
1) Metal ions
2) Coenzymes
Derived from vitamins
Antioxidants (neutralize free radicals)
Allosteric Activation
Allosteric Inhibition
Feedback Inhibition

5.6 Cell Membranes Show Selective Permeability
Concentration Gradient
In the absence of other forces, a substance moves from a region where it is highly concentrated to a region where it is less concentrated
“Down” the gradient from high to low
The net movement of a substance down a concentration gradient

Factors Affecting Diffusion Rate
Steepness of concentration gradient
Steeper gradient, faster diffusion
Molecular size
Smaller molecules, faster diffusion
Higher temperature, faster diffusion

5.6 Passive vs. Active Transport
Span the lipid bilayer
Can open to both sides
Change shape when they interact with solutes

Passive Transport
Flow of solutes through transport proteins down gradient
Does not require any energy input

Active Transport
Movement of solutes through transport proteinsup gradient
Transport protein must be activated
Uses ATP energy
Helps maintain membrane gradients (Ca+, Na+, K+) that are essential for:
Muscle contraction
Neuron function
Membrane Crossing: Overview

5.8 Movement of Water
OSMOSIS—diffusion of water molecules across a selectively permeable membrane
Effects of Tonicity
Hypertonic - having more solutes (low water conc.)
Isotonic—having the same amount of solutes (same water conc.)
Hypotonic – having fewer solutes (high water conc.)
Tonicity and Osmosis

Where It Starts – Photosynthesis
Chapter 6
6.1 Sunlight as an Energy Source
Photosynthesis uses a fraction of the electromagnetic spectrum
Visible light (380-750 nm)
Individual packets of light energy
Each type of photon has fixed amount of energy
Light-absorbing molecules
Absorb photons with particular wavelengths and transmit others
Color you see are the wavelengths not absorbed (reflected)
Variety of Pigments
Chlorophylls (green)
Carotenes (orange)
Xanthophylls (yellow)
Anthocyanins (purple)
Phycobilins (red or blue-green)

6.2 T.E. Englemann’s Experiment (1882)
Photosynthesis produces oxygen
Certain bacterial cells will move toward places where oxygen concentration is high
Movement of bacteria can be used to determine optimal light wavelengths for photosynthesis
Algal strand placed on microscope slide and illuminated by light of varying wavelengths
Oxygen-requiring bacteria placed on same slide
Bacteria congregated where red and violet wavelengths illuminated alga
Bacteria moved to where algal cells released more oxygen – areas illuminated by the most effective light for photosynthesis
Main pigments in most photoautotrophs

6.3 Photosynthesis
A two stage process
1)Light-dependent reactions
Occurs in the thylakoid membranes
2) Light-independent reactions
Occurs in the stroma
Photosynthesis Equation

Capture sunlight energy and use it to carry out photosynthesis
Some bacteria
Many protistans
Pigments in Photosynthesis
in plasma membranes
in thylakoid membranes of chloroplasts
associated with electron transfer chains

6.4 Light-Dependent Reactions
Converts light energy to chemical bond energy
Pigments absorb light energy, give up electrons that enter electron transfer chains
Water molecules are split, oxygen is released, ATP and NADPH are formed
ATP and NADPH Formation

6.6 Light-Independent Reactions
Energy from ATP and NADPH used to synthesize glucose from CO2 and H20
Light not required
Calvin-Benson Cycle
Overall reactants
Carbon dioxide
Overall products
Using the Products of Photosynthesis
Glucose is the building block for:
The most easily transported plant carbohydrate
The most common storage form

Linked Processes
Energy-storing pathway
Releases oxygen
Requires carbon dioxide

Aerobic Respiration
Energy-releasing pathway
Requires oxygen
Releases carbon dioxide

How Cells Release Chemical Energy
Chapter 7
7.1 Energy-Releasing Pathways
Anaerobic pathways
Evolved first
Don’t require oxygen
Start with glycolysis in cytoplasm
Completed in cytoplasm
Less efficient (2 ATPs / glucose)

Energy-Releasing Pathways
Aerobic pathways
Evolved later
Require oxygen
Start with glycolysis in cytoplasm
Completed in mitochondria
More efficient (36 ATPs / glucose)

7.2 Anaerobic and Aerobic Respiration Both Start with Glycolysis
Glycolysis occurs in cytoplasm
Catalyzed by enzymes
Glucose 2 Pyruvate
(6C) (3C)
Net Energy Yield from Glycolysis
Energy requiring steps:
2 ATP invested
Energy releasing steps:
2 NADH formed
4 ATP formed
Net yield is 2 ATP and 2 NADH

7.3 If oxygen is present…
Pyruvate enters a mitochondrion and is modified to become Acetyl-CoA
Kreb’s Cycle in a Mitochondrion

7.4 Electron Transfer Chain (ETC)
Occurs in the mitochondria
Coenzymes deliver electrons to electron transfer chains
Electron transfer sets up H+ ion gradients
Flow of H+ down gradient powers ATP formation
Oxygen is the final electron acceptor
Importance of Oxygen
ETC requires oxygen
Oxygen withdraws

Oxygen withdraws spent electrons from the ETC, then combines with H+ to form water

Summary of Transfers
ATP Accounting
2 ATP formed
Krebs cycle
2 ATP formed
Electron transfer phosphorylation
32 ATP formed
Overview of Aerobic Respiration

Efficiency of Aerobic Respiration
39% of the energy in glucose is conserved in the ATP formed
Most energy is lost as heat.
For comparison, most engines are less than 10% efficient

7.5 & 7.6 Anaerobic Pathways
Do not use oxygen
Produce less ATP than aerobic pathways (2 % efficient)
Two types of fermentation pathways
Alcoholic fermentation
Lactate fermentation
Alcoholic Fermentation
Begins with glycolysis
Does not break glucose down completely
Yields only the 2 ATP in glycosis
Steps that follow regenerate NAD+, produce CO2, and produce ethanol as a waste product, toxic above 10%

Alcoholic Fermentation
Single-celled fungi
Carry out alcoholic fermentation
Used to make bread, beer, and wine.

Lactate Fermentation
Begins with glycolysis
Does not break glucose down completely
Yields only the 2 ATP in glycolysis
Steps that follow regenerate NAD+ and produce lactate as a waste product
Bacteria and fast-twitch muscles
Lactobacillus used to make cheeses, yogurt, buttermilk, sour cream, sauerkraut
When demands for energy are immediate and intense and cells run out of oxygen, animal muscle cells use lactate fermentation
Lactic acid makes muscles sore

Chapter 8
How cells reproduce

8.1 Cell Division
nuclear division
cytoplasmic division

Nuclear division that occurs in somatic (body) cells
Asexual reproduction
Produces two cells that are identical to each other and to the original cell.
Chromosome—a molecule of DNA and its proteins
Chromosomes must be duplicated before nuclear division

8. 2 Cell Cycle
Cell cycle—a cycle starts when a new cell forms.
Includes Interphase
Includes Mitosis
(prophase, metaphase, anaphase, telophase)

The longest portion of the cell cycle
Three stages
G1—cell growth
S—DNA replication
G2—preparations for division

8.3--A closer look at mitosis
Chromosomes condense
Microtubules form a bipolar spindle
Nuclear envelope breaks up
All chromosomes are aligned midway between the spindle poles (at the cell’s equator)
Anaphase—Microtubules move sister chromatids of each chromosome apart, to opposite poles
A new nuclear envelope forms around each of two groups of chromosomes as they decondense.
Things to remember about mitosis
Mitosis produces two cells from one cell
All cells are exactly the same
They have the same number of chromosomes

8.4 Cytoplasm Division

Cleavage—cytoplasm pinches in two.
Occurs after mitosis is over.
Microfilaments attach to the plasma membrane and contract.

Cell plate formation
Occurs after mitosis is over.
Vesicles fuse at the former equator
Cellulose accumulates
Plasma membrane forms

8.5 When Control Is Lost
Growth and reproduction depend on controls over cell division
Checkpoint proteins:
Mitosis inhibitors—tumor suppressors
Mitosis stimulators—oncogenes
When checkpoints fail, unregulated growth occurs
Ex: Neoplasms
Abnormal masses of cells
Benign – grow slowly and retain surface recognition proteins that keep them in a home tissue (noncancerous)
Malignant – grow and divide abnormally, disrupting surrounding tissues physically and metabolically (cancerous)
The process of abnormal cell migration and tissue invasion
The way cancer cells spread
HeLa Cells
Line of human cancer cells that can be grown in culture
Descendents of tumor cells from a woman named Henrietta Lacks
Lacks died at 31, but her cells continue to live and divide in labs around the world
Culturing Cells
Growing cells in culture allows researchers to investigate processes and test treatments without danger to patients
Taxol—anticancer drug derived from Pacific Yew

Meiosis and Sexual Reproduction
Chapter 9
9.1 Asexual vs. Sexual Reproduction
One parent produces offspring via mitosis
All offspring are genetically identical to one another and to parent (clones)
No genetic variation
Gamete production
Produces genetic variation among offspring

Genes and alleles
Gene—a section of DNA in a chromosome that codes for a heritable trait.
Allele—one of two or more forms of a gene that specify different versions of the same trait.

Sexual Reproduction
Through sexual reproduction, offspring inherit new combinations of alleles, which leads to variations in traits
This variation in traits is the basis for evolutionary change

Chromosome number Humans have 46 (23 pairs)
Diploid vs. Haploid
Diploid (2n)—having two of each type of chromosome
Haploid (n)—having only one of each type of chromosome

9.2 Homologous Chromosomes Carry Different Alleles
Diploid cell has two of each chromosome
One chromosome in each pair from mother, other from father
Paternal and maternal chromosomes carry different alleles
Chromosome Number
Sum total of chromosomes in a cell
Germ cells are diploid (2n)
Gametes are haploid (n)
Meiosis halves chromosome number
Gamete Formation
Gametes are sex cells (egg and sperm)
Arise from germ cells
Animals produce gametes directly
Gamete Formation
Plants produce gametes indirectly
Plants produce spores that mature into gametophytes
Gametophytes give rise to gametes

9.3 Meiosis: Two Divisions
Two consecutive nuclear divisions
Meiosis I
Meiosis II
DNA is not duplicated between divisions
Four haploid nuclei are formed
The two sister chromatids of each duplicated chromosome are separated from each other

Stages of Meiosis

Meiosis I
Prophase I, Metaphase I, Anaphase I, Telophase I

Meiosis II
Prophase II, Metaphase II, Anaphase II, Telophase II

Meiosis I - Stages
Prophase I
Each duplicated chromosome pairs with its homologue
Homologues swap segments (crossing over)
Microtubules attach to chromosomes as spindles form.
Metaphase I
Chromosomes line up in the middle of cell
The spindle is now fully formed
Anaphase I
Homologous chromosomes are separated
The sister chromatids of each chromosome remain together
Telophase I
The chromosomes arrive at opposite poles
The cytoplasm divides
There are now two haploid cells
This completes Meiosis I

Meiosis II - Stages
Prophase II
Microtubules attach to the kinetochores of the duplicated chromosomes
Chromosomes move toward the spindle’s equator
Metaphase II
All of the duplicated chromosomes are lined up at the spindle equator, midway between the poles
Anaphase II
Sister chromatids separate to become independent chromosomes
Separated chromosomes move to opposite poles
Telophase II
The chromosomes arrive at opposite ends of the cell
A nuclear envelope forms around each set of chromosomes
The cytoplasm divides
There are now four haploid cells

9.4 Crossing Over
Effect of Crossing Over
After crossing over, each chromosome contains both maternal and parental segments
Creates new allele combinations in offspring
Random Alignment
Initial contacts between microtubules and chromosomes are random
Either the maternal or paternal member of a homologous pair can end up at either pole
The chromosomes in a gamete are a mix of chromosomes from the two parents
Possible Chromosome Combinations
As a result of random alignment, the number of possible combinations of chromosomes in a gamete is:
(n is number of chromosome types)
23 = 8 246 = 7.04 X 1013 (70 trillion)

Male and female gametes unite and nuclei fuse
Fusion of two haploid nuclei produces diploid nucleus in the zygote
Which two gametes unite is random
Adds to variation among offspring

Factors Contributing to Variation among Offspring
Crossing over during prophase I
Random alignment of chromosomes at metaphase I
Random combination of gametes at fertilization

Prophase I (Meiosis)
Homologous pairs interact and crossing over occurs

Prophase (Mitosis) and Prophase II (Meiosis)
Homologous pairs do not interact

Anaphase I (Meiosis)
Homologous chromosomes are separated

Anaphase (Mitosis) and Anaphase II (Meiosis)
Sister chromatids of a chromosome are separated

Results of Mitosis and Meiosis
1 diploid cell to 2 diploid cells
1 haploid to 2 haploid cells
Each identical to parent
1 diploid cell to 4 haploid cells
Each different from parent and different from one another

Mitosis & Meiosis Compared
Asexual reproduction
Growth, repair
Occurs in somatic cells
Produces clones

Sexual reproduction
Occurs in germ cells
Produces variable offspring

9.5 Life Cycles
Animal vs. Plant Life Cycle

Observing Patterns in Inherited Traits
Chapter 10
10.1Early Ideas about Heredity
People knew that sperm and eggs transmitted information about traits
Blending theory
Would expect variation to disappear
Variation in traits persists

Gregor Mendel
Strong background in plant breeding and mathematics
Using pea plants, he found indirect evidence of how parents transmit genes to offspring
The Garden Pea Plant
True breeding
Can be experimentally cross-pollinated

Genetic Terms
Units of information about specific traits
Passed from parents to offspring
Each has a specific location (locus) on a chromosome
Different forms of a gene--Arise by mutation
Dominant allele masks a recessive allele that is paired with it

Allele Combinations
having two identical alleles at a locus
AA or aa
having two different alleles at a locus

Genotype & Phenotype
Genotype refers to particular genes an individual carries (AA, Aa, aa)
Phenotype refers to an individual’s observable traits (red, pink, white)
Cannot always determine genotype by observing phenotype

Tracking Generations
Parental generation P
mates to produce
First-generation offspring F1
mate to produce
Second-generation offspring F2

10.2Monohybrid Crosses
Use F1 offspring of parents that breed true for different forms of a trait:(AA x aa = Aa)
A cross between two F1 heterozygotes, which are the “monohybrids” (Aa x Aa)
Monohybrid Crosses
F1 Results of One Monohybrid Cross
F2 Results of Monohybrid Cross

The chance that each outcome of a given event will occur is proportional to the number of ways that event can be reached
Punnett Square of a Monohybrid Cross
Mendel’s Monohybrid Results
Individual that shows dominant phenotype is crossed with individual with recessive phenotype (AA X aa) or (Aa X aa)
Examining offspring allows you to determine the genotype of the dominant individual
Mendel’s Theory of Segregation
Diploid cells have pairs of alleles
The two alleles are separated during meiosis
They end up in different gametes
“For a given trait, alleles separate”

10.3 Dihybrid Cross
Experimental cross between individuals that are homozygous for different versions of two traits
Dihybrid Crosses
Independent Assortment
Mendel’sTheory of Independent Assortment
A given pair of alleles is sorted into one gamete or another independently of alleles on other chromosomes.

CODOMINANCE--A pair of non-identical alleles affecting two phenotypes are expressed at the same time
Ex: ABO blood groups
Genetics of ABO Blood Types: Three Alleles
Gene that controls ABO type codes for enzyme that dictates structure of a glycolipid on blood cells
Two alleles (IA and IB) are codominant when paired
Third allele (i) is recessive to others
ABO and Transfusions
Recipient’s immune system will attack blood cells that have an unfamiliar glycolipid on surface
Type O is universal donor because it has neither type A nor type B glycolipid
Type AB is the universal recipient

10.5 Linkage Groups
All the genes on one chromosome are called a linkage group.
If no crossing over occurs, genes on the same chromosome will be inherited together
Crossover Frequency

10.6 Genes and the Environment
Environmental conditions affect the expression of genes
Phenotypic plasticity
Yarrow, Aspen
Himalayan rabbits
Leaf chemicals
Genes and the Environment
Himalayan rabbits are white, but are homozygous for an allele that produces melanin in cool areas of the body

10.7 Complex Variations in Traits

Continuous Variation
A more or less continuous range of small differences in a given trait among individuals
The greater the number of genes and environmental factors that affect a trait, the more continuous the variation in versions of that trait
Human Variation
Some human traits occur as a few discrete types
Attached or detached earlobes
Many genetic disorders
Other traits show continuous variation
Eye color
Describing Continuous Variation

Chromosomes and Human Genetics
Chapter 11
11.1 Autosomes vs. Sex chromosomes
Autosomes—chromosomes that are the same in both sexes
Sex chromosomes—determine gender, different in females and males
Sex Chromosomes
In mammals and fruit flies:
XX is female, XY is male
In birds, butterflies, moths, some fish:
XY is female, XX is male
Human X and Y chromosomes function as homologues during meiosis

Sex Determination
The Y Chromosome
Fewer than two dozen genes identified
One is the gene for male sex determination
SRY gene (sex-determining region of Y)
SRY present, testes form
SRY absent, ovaries form
Effect of Y Chromosome
The X Chromosome--Carries more than 2,062 genes
Most genes deal with traits expressed both in females and males

A preparation of an individual’s chromosomes
The cell cycle is stopped during metaphase
Chromosomes are stained and photographed

11.2 & 11.7 Human Genetic Analysis
Geneticists gather information from several generations
If a trait follows a simple Mendelian inheritance pattern they can predict the probability of the trait showing up again
Chart that shows genetic connections among individuals
Standardized symbols
Genetic Abnormality
A rare or uncommon version of a trait
Example: Polydactyly
Unusual number of toes or fingers
Does not cause any health problems
Genetic Disorder
Inherited condition that causes mild to severe medical problems
Why don’t they disappear?
Mutation introduces new rare alleles
In heterozygotes, the harmful allele may not be expressed, but still be passed on to offspring
Disorder may not be expressed until after reproduction
Patterns of InheritanceAutosomal Dominant Inheritance
Trait typically appears in every generation
Examples of autosomal dominant disorders
Huntington’s disease—nervous system degeneration
Machado-Joseph disease—loss of muscle control
Familial hypercholestorolemia—very high cholestorol levels
Autosomal Recessive Inheritance Patterns
Carriers possible
Two carriers have a 25% of having an affected child.
Examples of autosomal recessive disorders
Albinism—absence of pigments
Cystic fibrosis—Causes progressive disability and early death, may require lung transplants. Characterized by shortness of breath, frequent lung and sinus infections, failure to thrive, diarrhea, and infertility. Most common among Caucasians and Ashkenazi Jews

11.4 X-Linked Inheritance
Males show disorder more than females
Son cannot inherit disorder from his father
Examples of X-Linked Traits
Color blindness
Inability to distinguish among some of all colors
Blood-clotting disorder
Common in European royal families

11.5 Altered Chromosomes
A linear stretch of DNA is reversed
within the chromosome
Loss of some segment of a chromosome
Most are lethal or cause serious disorder
A piece of one chromosome becomes attached to another nonhomologous chromosome
Most are reciprocal
Philadelphia Chromosome
Philadelphia chromosome arose from a reciprocal translocation between chromosomes 9 and 22
First chromosomal abnormality to be associated with a cancer (leukemia)
Does Chromosome Structure Evolve?
Alterations in the structure of chromosomes generally are not good and tend to be selected against
Over evolutionary time, however, many alterations with neutral effects became built into the DNA of all species

11.6 Changes in Chromosome Number--Aneuploidy
Individuals have one extra or less chromosome
(2n + 1 or 2n - 1)
Major cause of miscarriages in humans

Autosomal Aneuploidy
Down Syndrome (Trisomy of chromosome 21)
Mental impairment
Can be detected before birth
Risk of Down syndrome increases dramatically in mothers over age 35
Aneuploidy involving sex chromosomes
Turner Syndrome (XO)
Klinefelter Sydrome (XXY)
Individuals have three or more of each type of chromosome (3n, 4n)
Common in flowering plants
Lethal for humans
99% die before birth
Newborns die soon after birth

11.8 Genetic Screening
Large-scale screening programs detect affected persons
Newborns in United States routinely tested for PKU
Early detection allows dietary intervention and prevents brain impairment
Phenotypic Treatments
Symptoms of many genetic disorders can be minimized or suppressed by
Dietary controls
Adjustments to environmental conditions
Surgery or hormonal treatments
Genetic Counseling
Genetic counseling is available to help parents-to-be make informed decisions.

DNA Structure and Function
Chapter 12
12.2 DNA is made of nucleotides
Each nucleotide consists of
Deoxyribose (5-carbon sugar)
Phosphate group
A nitrogen-containing base
Four bases
Adenine, Guanine, Thymine, Cytosine

Composition of DNA
Amount of adenine relative to guanine differs among species
Amount of adenine always equals amount of thymine and amount of guanine always equals amount of cytosine
A=T and G=C
Patterns of Base Pairing

12.4 DNA Replication
DNA is two nucleotide strands held together by hydrogen bonds
H bonds are easily broken
Each single strand then serves as template for new strand
Semiconservative Replication
Base Pairing during Replication
Enzymes in Replication
Enzymes unwind the two strands
DNA polymerase attaches complementary nucleotides
DNA ligase fills in gaps
Enzymes wind two strands together
DNA Repair
Mistakes can occur during replication
DNA polymerase and DNA ligase can repair mistakes on the new strand

12.5 Cloning What is a key functional difference between plant and animal cells?
Plant cells are generally totipotent while animal cells generally are not.
Totipotency—”total potential”
The ability of one cell to produce all the different types of a cell in an organism
Totipotency of plant cells
Animals cell are more limited
Most animal cells can’t de-differentiate and become other types of cells once they’ve specialized and matured into skin cells, liver cells, etc.
Embryonic stem cells--totipotent
Blastocyst embryonic stem cells--totipotent
Over 100 million Americans suffer from diseases that are prime candidates for stem cell research
heart disease, cancer, diabetes, Parkinson''s disease, Alzheimer''s disease, autoimmune diseases
Embryos are donated by couples using in vitro fertilization
1) Are these frozen embryos human life, and therefore, something precious to be protected?
2) Shouldn''t they be used for a greater good, for research that has the potential to save and improve other lives if they’re going to be discarded or destroyed otherwise?
Stem cells can also be derived from certain mature animal cells
Umbilical cord stem cells—multipotent
Adult stem cells—multipotent

Unfertilized eggs—somatic cell nuclear transfer
Remove genetic material from an egg (its 23 chromosomes)
Transplant 46 chromosomes from one specialized adult cell
Stem cell technology and somatic nuclear transfer can both be used to make new individuals or simply new cells.
Making a genetically identical copy of an individual
Researchers have been creating clones for decades
These clones were created by embryo splitting

Dolly: Cloned from an adult cell--Somatic nuclear transfer
Showed that differentiated cells could be used to create clones
Sheep udder cell was combined with enucleated egg cell
Dolly is genetically identical to the sheep that donated the udder cell
More Clones
Mice, Cows, Pigs, Goats, Cats, Guar

Major problem with cloning
No genetic variation
Plant cells clone more easily than do animal cells

Late blight of potato
The people of Ireland relied heavily on one variety of potatoes called “lumpers”
The vegetatively propagated potatoes were all clones--no genetic variation
Late blight of potato
A water mold, Phytophthora infestans, infected the island and decimated the entire crop for multiple years
1 million people died from starvation
At least 1 million left the island
Crops with genetic variation are less vulnerable to changing conditions

From DNA to Proteins
Chapter 13
13.1From DNA to Proteins
Two steps produce all proteins:
1) DNA is transcribed to form RNA
Occurs in the nucleus
2) RNA is translated to form polypeptide chains, which fold to form proteins
Occurs in the cytoplasm

Three Classes of RNAs
Messenger RNA (mRNA)
Carries protein-building instructions
Ribosomal RNA (rRNA)
Major component of ribosomes
Transfer RNA (tRNA)
Delivers amino acids to ribosomes

A Nucleotide Subunit of RNA
RNA Base Pairing during Transcription
As in DNA, Cytosine (C) pairs with Guanine (G)
But Adenine (A) pairs with Uracil (U)
RNA contains no Thymine (T)

A base sequence in the DNA that signals the start of a gene
For transcription to occur an enzyme (RNA polymerase) must bind to a promoter
Adding Nucleotides
Transcript Modification

13.2 & 13.3 Genetic Code
Nucleotide bases read in blocks of three
Code Is Redundant
Twenty kinds of amino acids are specified by 64 codons
Most amino acids can be specified by more than one codon
Six codons specify leucine

tRNA Structure
Ribosomes made of rRNA

13.4 Three Stages of Translation
Initiation, Elongation, Termination

Initiator tRNA binds to small ribosomal subunit
The complex attaches to mRNA and moves along it to an AUG “start” codon
Large ribosomal subunit joins complex
Binding Sites on Large Subunit
mRNA passes through ribosomal subunits
tRNAs deliver amino acids to the ribosomal binding site in the order specificied by mRNA
Peptide bonds form between the amino acids and the polypeptide chain grows
In response to a STOP codon:
--mRNA is released from the ribosome
--new polypeptide is released
--the two ribosomal subunits separate

What Happens to the New Polypeptides?
Some are used the cytoplasm
Others enter the endoplasmic reticulum and are modified

13.5 Gene Mutations
Small-scale changes in the nucleotide sequence of a DNA molecule
--Base-Pair Substitutions
Frameshift Mutations
Extra base added into gene region
Base removed from gene region
Both shift the reading frame
Result in many wrong amino acids

Mutations in Genes
Spontaneous Mutation Rates
Average rate for eukaryotes is between 10-4 and 10-6 per gene per generation
Only mutations that arise in germ cells can be passed on to next generation
Factors that increase rates of mutations
Ionizing radiation
Nonionizing radiation
UV radiation
Alkylating agents
Cigarette smoke

Harmful, Neutral, Beneficial
Depending on the organism’s environment

Studying and Manipulating Genomes
Chapter 15
15.5 Genetic Changes
Humans have been indirectly modifying the genetics of other species for thousands of years
Artificial selection (breeding) of plants and animals
The direct study and manipulationof genes and gene function in humans and other organisms.

15.6-15.8 Genetic Engineering
Genes are isolated, modified, and inserted into an organism
Made possible by recombinant technology
GMO = genetically modified organism
Engineered Plants
Cotton plants that display resistance to herbicide
Aspen plants that produce less lignin and more cellulose
Tobacco plants that produce human proteins
Mustard plant cells that produce biodegradable plastic
Engineered Animals
Human genes are inserted into mice to study molecular basis of genetic disorders, such as Alzheimer’s disease
Reverse dwarfism in mice
Produce fluorescent mice
Goats that produce human anti-clotting factors
Transferring an organ from one species into another
Researchers have altered a gene in pigs so that pig organs may not be rejected by the human immune system
What about the transfer of viruses across species? Avian flu, swine flu, etc.

15.9 Where Do We Go Now?
Can we bring about beneficial changes without harming ourselves or the environment?
GMOs as crops
Many crops (cotton, soybean, corn) are genetically modified
GMOs as crops

What if engineered genes escape into other species in natural populations?

15.10 Eugenic Engineering--Human Gene Therapy
Selecting “desirable” human traits
Who decides what is desirable?

Evidence of Evolution
Chapter 16
Why study evolution? "Nothing in biology makes sense except in the light of evolution." T. Dobzhansky
A unifying principle that explains so many of the “whys” in biology :
1) Why new species originate.
2) Why there is such diversity among living things.
3) Why different species share key characteristics.
4) Why species are adapted their environment.

What is evolution? “Descent with modification”

16.1 Early Beliefs, Confounding Discoveries
Early Europeans (14th Century) held the Aristotelian belief that each species was perfect and immutable.
Comparative morphology
Size of the known world expanded tremendously in the 15th century
Discovery of new organisms in previously unknown places could not be explained by accepted beliefs
Comparative Morphology
Study of similarities and differences in body plans of major groups
Puzzling patterns:
Animals as different as dolphins and bats have similar bones in forelimbs
Some parts seem to have no function
How do you explain a snake pelvis, the ankle bones of a whale, or your own tailbone?
Similar rock layers throughout world
Certain layers contain fossils
Deeper layers contain simpler fossils than shallow layers
Some fossils seem to be related to living species

16.2 19th Century - New Theories
Scientists attempt to reconcile evidence of change with traditional belief that species are perfect and immutable.
Two examples
Georges Cuvier - multiple catastrophes
Jean Lamarck - inheritance of acquired characteristics
Charles Darwin
At age 22, Charles Darwin began a five-year, round-the-world voyage aboard the Beagle
As the ship’s naturalist he collected and examined the species that inhabited the regions the ship visited
Voyage of the Beagle

16.3 Darwin’s Theory Takes Form
GALAPAGOS Volcanic islands far off coast of Ecuador
Darwin found many new species there that had evolved from continental ancestors
Galapagos Finches
Darwin observed 13 new species of finches with a variety of lifestyles and body forms
He attempted to correlate variations in their traits with the environmental challenges they faced
Descent with modification
In Argentina, Darwin observed fossils of extinct glyptodonts
Glyptodonts resembled living armadillos
The Theory of Uniformity
Principles of Geology by Charles Lyell
Theory of Uniformity--gradual, repetitive processes have shaped the Earth more than rare catastrophes
Challenged the view that Earth was only 6,000 years old
Malthus - Struggle to Survive
Thomas Malthus, a clergyman and economist, wrote an essay that Darwin read on his return to England
Argued that as population size increases, resources dwindle, and the struggle to live intensifies
Darwin’s Theory of Evolution by Natural Selection
A population can change over time when individuals differ in heritable traits that affect the ability to survive and reproduce
Alfred Wallace
Naturalist who worked in Madagascar
Arrived at the same conclusions Darwin did
Wrote to Darwin describing his views
Prompted Darwin to formally present his work
On the Origin of Species
Darwin’s book
Published in 1859
Detailed evidence supporting evolution and speciation by natural selection

16.4 Fossils
Recognizable, physical evidence of organisms that lived in the distant past
Direct or indirect evidence
Organism becomes buried in ash or sediments
Rapid burial and a lack of oxygen aid in preservation
The organic remains become infused with metal and mineral ions
Fossils are found in sedimentary rock
This type of rock is formed in layers
In general, layers closest to the top were formed most recently
Evidence of Past Life
Excavations unearthed similar fossil sequences in distant places
Scholars began to see connections between the Earth’s history and the history of life
Fossil record is incomplete
Species that had large bodies, hard bodies or parts, dense populations, wide distributions, or persisted for a long time period are over-represented in the fossil record.

16.5 Determining the age of fossils
Relative dating—fossils from lower rock layers are older than fossils from higher layers.
Absolute dating—using radiometric dating to assign an actual age to a fossil
Radiometric Dating
Carbon 14
Uranium 238
The time it takes for half of a quantity of a radioisotope to decay
C-14 = 5,730 years
U-238 = 4.5 billion years
Radiometric Dating
Geologic Time Scale
Phanerozoic eon
Cenozoic era—primates, horses
Mesozoic era—dinosaurs, birds, higher plants
Paleozoic era—insects, fish, algae, ferns
Proterozoic eon—eukaryotes, oxygen accumulates
Archean eon--prokaryotes

16.6 Evidence from Biogeography
Idea that the continents were once joined and have “drifted” apart
Initially based on the shapes
Pangea: supercontinent
Evidence of Movement
Glacial deposits

16.6 Evidence from Biogeography
Idea that the continents were once joined and have “drifted” apart
Initially based on the shapes
Pangea: supercontinent
Evidence of Movement
Glacial deposits
Fossils and mineral deposits
Magnetic orientation of rocks
Discovery of seafloor spreading provided a possible mechanism
Plate Tectonics
Earth’s crust is fractured into plates
Movement of plates is driven by upwelling of molten rock at mid-oceanic ridges
As seafloor spreads, older rock is forced down into trenches
Forces of Change
Supercontinent preceding Pangea
Same series of glacial deposits, coal seams, basalt, and fossils (seed ferns and land reptiles) are found in distantly separated continents
Changing Land Masses

16.7 Evidence from Comparative Morphology
Comparing body forms and structures of major lineages
Morphological Divergence
Change from the body form of a common ancestor
Homologous structure—similar body part that occurs in different species as a result of descent from a common ancestor (may serve different functions)
Morphological Divergence
Morphological Convergence
Individuals of different lineages evolve in similar ways under similar environmental pressures
Analogous structures—may serve similar functions but are not derived from a recent common ancestor

16.8 Comparative Development
Each animal or plant proceeds through a series of changes in form as it develops
Similarities in these stages may be clues to evolutionary relationships
Mutations that disrupt a key stage of development are selected against
Developmental Similarities
Proportional Changes in Skull

16.9 Comparative Biochemistry—Best Evidence for Evolution
Kinds and numbers of biochemical traits that species share is a clue to how closely they are related
Can compare DNA, RNA, or proteins
More similarity means species are more closely related
Comparing Proteins
Compare amino acid sequence of proteins produced by the same gene
Human cytochrome c
Identical amino acids in chimpanzee protein
Chicken protein differs by 18 amino acids
Yeast protein differs by 56
Sequence Conservation
Cytochrome c functions in electron transport
Deficits in this vital protein would be lethal
Long sequences are identical in yeast, wheat, and primates
Sequence Conservation
Nucleic Acid Comparison
Use single-stranded DNA or RNA
Hybrid molecules are created, then heated
The more heat required to break hybrid, the more closely related the species

16.10 Taxonomy
Field of biology concerned with identifying, naming, and classifying species
Binomial system of nomenclature
Devised by Carolus Linnaeus
Each species has a two-part Latin name
First part is generic (genus)
Second part is specific name (species)
Higher Taxa
Kingdom, Phylum, Class, Order, Family, Genus, Species
The scientific study of evolutionary relationships among species
We can learn more about a species by studying its close relatives
Six-Kingdom Scheme is Problematic
Three-Domain Classification

16.12 Evolutionary Tree of Life

Processes of Evolution
Chapter 17
17.1 Populations Evolve
Biological evolution does not change individuals, it changes a population
Heritable traits in a population vary among individuals
Individuals better-suited to their environment pass more of their alleles on to the next generation
Evolution is the change in allele (gene) frequencies of a population
Population and Species
A group of individuals of the same species occupying a given area
A group of organisms that can interbreed to produce fertile offspring
What Determines Alleles in New Individual?
produces new alleles
Crossing over at meiosis I
Independent assortment
reshuffle alleles present in a gene pool
The Gene Pool
All of the genes in the population
A genetic resource shared by all members of population
Fitness—not just aerobics anymore
“Success” in the biological world = FITNESS
Passing relatively more genes on to the next generation
Well-suited to your environment

17.2 Genetic Equilibrium
When allele frequencies are not changing
Population is not evolving
Genetic equilibrium requires all 5
No mutation
No natural selection
No sexual selection (random mating)
No immigration/emigration
No genetic drift
No Change through Generations
Hardy-Weinberg Rule
At genetic equilibrium, proportions of genotypes at a locus with two alleles are given by the equation:
p + q = 1
p2 + 2pq + q2 = 1
Frequency of allele A = p
Frequency of allele a = q
Punnett Square
Frequencies in Gametes

17.3 Microevolutionary Processes
Drive a population away from genetic equilibrium
Small-scale changes in allele frequencies brought about by:
Natural selection
Sexual selection (non-random mating)
Immigration or Emigration
Genetic drift

17.4 Directional Selection
Allele frequencies shift in one direction
Pesticide Resistance
Pesticides kill susceptible insects
Resistant insects survive and reproduce
If resistance has heritable basis, it becomes more common with each generation
Antibiotic Resistance
Overuse of antibiotics has led to an increase in resistant forms
Most susceptible bacteria die out and are replaced by resistant forms

17.5 Stabilizing Selection
Intermediate forms are favored and extremes are eliminated
Stabilizing Selection: An Example
Disruptive Selection
Forms at both ends of the range of variation are favored
Intermediate forms are selected against
Ex: Black-bellied seedcracker

17.6 Sexual Selection
Selection favors certain secondary sexual characteristics
Through nonrandom mating, alleles for preferred traits increase
Leads to increased sexual dimorphism
Balanced Polymorphism
Polymorphism - “having many forms”
Occurs when two or more alleles are maintained at high frequencies
Sickle-Cell Trait: Heterozygote Advantage
Heterozygotes develop a more mild form of sickle-cell anemia than do homozygotes (AA)
Heterozygotes are more resistant to malaria than homozygotes (aa)

17.7 Genetic Drift
Random change in allele frequencies brought about by chance
Effect is most pronounced in small populations
Computer Simulation
Computer Simulation
A severe reduction in population size
Causes pronounced drift
Examples: Elephant seals, Cheetah, Many endangered species, Florida Panther
Populations recover faster than genetic variation
Founder Effect
Effect of drift when a small number of individuals start a new population
By chance, allele frequencies of founders may not be same as those in original population
Nonrandom mating between related individuals
Leads to increased homozygosity
Can lower fitness when deleterious recessive alleles are expressed

17.8 Gene Flow
Physical flow of alleles in a population
Tends to keep the gene pools of populations similar
Counters the differences that result from mutation, natural selection, and genetic drift

17.9 Speciation & Species
Natural selection can lead to speciation
Speciation can also occur as a result of other microevolutionary processes
Genetic drift
Morphology & Species
Morphological traits may not be useful in distinguishing species
Members of same species may appear different because of environmental conditions
Morphology can vary with age and gender
Different species can appear identical
Variable Morphology
Biological Species Concept
“Species are groups of interbreeding natural populations that are reproductively isolated from other such groups.”
- Ernst Mayr
If gene flow ends, genetic divergence begins
Gene flow keeps two populations from diverging
If gene flow stops, differences between gene pools gradually accumulate
Natural selection, genetic drift, and mutation can contribute to divergence
Reproductive Isolation
Cornerstone of the biological species concept
Speciation is the attainment of reproductive isolation
Reproductive isolation arises as a by-product of genetic change
Mechanisms of Reproductive Isolation
Pre-zygotic isolation
Mating or zygote formation is prevented
Post-zygotic isolation
Takes effect after hybrid zygotes form
Zygotes may die early, be weak, or be sterile
Prezygotic Isolation
Mechanical Isolation
Behavioral Isolation
Temporal Isolation
Ecological Isolation
Gamete Mortality
Postzygotic Mechanisms
Zygotic mortality
Hybrid inviability
Hybrid sterility

17.10 Mechanisms of Speciation
Allopatric speciation
Sympatric speciation
Parapatric speciation
Allopatric Speciation
Speciation in geographically isolated populations
Probably most common mechanism of speciation
Some sort of barrier arises and prevents gene flow
Extensive Divergence Prevents Interbreeding
Species separated by geographic barriers will diverge genetically
If divergence is great enough it will prevent interbreeding even if the barrier later disappears
Allopatric Speciation in Archipelagos
Island chains some distance from continents
Galapagos Islands (Darwin’s finches)
Hawaiian Islands
Colonization of islands followed by genetic divergence sets the stage for speciation
Volcanic origins, variety of habitats
Adaptive radiations:
Honeycreepers - In absence of other bird species, they radiated to fill numerous niches
Fruit flies (Drosophila) - 40% of fruit fly species are found in Hawaii

17.11 Speciation without a Barrier
Sympatric speciation
ancestral and derived species share the same range
Examples: polyploidy and Cichlids
Sympatric Speciation by Polyploidy
Change in chromosome number (3n, 4n, etc.)
Offspring with altered chromosome number cannot breed with parent population
Common mechanism of speciation in flowering plants
Sympatric Speciation in African Cichlids
Multiple species of African Cichlids evolved in the same lake
Parapatric speciation
Adjacent populations evolve into distinct species while maintaining contact along a common border
Parapatric Speciation
Examples: Tasmanian velvet worms, Cottonwoods

17.12 Macroevolution We’re All Related
All species are related by descent
Share genetic connections that extend back to the origin of life
Evolutionary Tree (Phylogeny)
A phylogeny is a tree, not a ladder
Gradual Model
Speciation model in which species emerge through many small morphological changes that accumulate over a long time period
Punctuation Model
Speciation model in which most changes in morphology are compressed into brief period near onset of divergence
Adaptive Radiation
Burst of divergence
Single lineage gives rise to many new species
New species fill vacant adaptive zone
Adaptive zone is “way of life” or niche
Success may hinge on a “key innovation”
Irrevocable loss of a species
Mass extinctions have played a major role in evolutionary history
Fossil record shows 20 or more large-scale extinctions
Reduced diversity is followed by adaptive radiation
Who Survived?
Species survival was to some extent random
Asteroids have repeatedly struck Earth destroying many lineages
Changes in global temperature favored lineages that are widely distributed
Human-caused extinctions
Since extinction is natural, is there anything wrong with letting endangered species go extinct today?

17.14 Adaptation & the Environment
An adaptation is any heritable aspect of form, function, behavior, or development that improves the odds of surviving and reproducing in a given environment

The Origin and Early Evolution of Life
Chapter 18
18.1 The Big Bang
12-15 billion years ago all matter was compressed into a space the size of our sun
Sudden instantaneous distribution of matter and energy throughout the known universe
Temperatures dropped billions of degrees
Gaseous particles condensed into the first stars
The star of our solar system—the sun—formed 5 billion years ago.
Earth Forms
About 4.6 and 4.5 billion years ago
Minerals and ice orbiting the sun started clumping together
Heavy metals moved to Earth’s interior, lighter ones floated to surface
Produced outer crust and inner mantle
First Atmosphere
Hydrogen gas
Carbon monoxide
Carbon dioxide
No gaseous oxygen
Earth Is Suitable for Life
Large enough in diameter to hold onto an atmosphere
Close enough to the sun that water is not permanently frozen
Far enough from the sun that water doesn’t evaporate entirely
Stanley Miller’s Experiment
Mixed methane, hydrogen, ammonia, and water
Simulated lightning
Amino acids and other small molecules formed spontaneously

18.2 Where Did Cells Originate?
In areas where spontaneously assembled enzymes, ATP, and organic compounds were in close association
Clay flats—contain mineral ions that attract amino acids and nucleotides
Hydrothermal vents—oxygen-poor areas with iron-sulfide chambers that favor membrane formation
Proto-cells—simple membrane-bound sacs that enclosed metabolic machinery and were self-replicating
Have been formed experimentally
Possible Model
RNA World
RNA may have been the first genetic material
RNA is more simple than DNA so it likely assembled first
However, DNA is more stable and can carry more information so DNA was favored by natural selection.

18.3 First Cells
Originated in Archaean Eon (3.8 bya)
Were prokaryotic heterotrophs
Anaerobic respiration
No oxygen present
Early Proterozoic Eon
Origin of photosynthetic bacteria
Oxygen accumulates in atmosphere
Origin of aerobic respiration
Mats of cyanobacteria (photosynthetic prokaryotes)
Abundant 2.7 bya
2.1 bya

18.4 Eukaryotes have organelles
Nuclear envelope may have helped to protect genes from competition with foreign DNA
ER may have similarly protected and channeled vital proteins
Origin of the nucleus and ER
Origin of Mitochondria and Chloroplasts--Theory of Endosymbiosis
Mitochondria and chloroplasts are the descendents of free-living prokaryotic organisms
Prokaryotes were engulfed by early eukaryotes and became permanent internal symbionts

18.5 Evolutionary Tree

Population Ecology
Chapter 26
26.1 & 26.2
Population -- A group of individuals of the same species occupying a given area
Populations can be described in terms of:
Age structure, density, distribution, size
These vital statistics are called demographics

Population Age Structure
Populations divided into age categories
The reproductive base of a population includes first two categories

Density & Distribution
Density--number of individuals in some specified area of habitat
Distribution—pattern in which the individuals are dispersed

Determining Population Size
Direct counts are most accurate but seldom feasible
Can sample an area, then extrapolate
Capture-recapture method is used for mobile species

26.3Changes in Population Size
Immigration adds individuals
Emigration subtracts individuals
Births add individuals
Deaths subtract individuals
Per Capita Rates
Rates per individual
Total number of events in a time interval divided by the number of individuals
Per capita birth rate per month = Number of births per month / Population size
Zero Population Growth
When number of births is balanced by number of deaths
Population size remains stable
Net reproduction per individual per unit time
Variable combines per capita birth and death rates
Used to calculate rate of growth of a population
Exponential Growth Equation
G = rN
G = population growth
r = net reproduction per individual
N = population size
Exponential Growth
The larger the population gets, the faster it grows
J-shaped curve
Exponential Growth in Field Mice
Effect of Deaths
Population will grow exponentially as long as per capita death rates are lower than per capita birth rates
Biotic Potential
Maximum rate of increase per individual under ideal conditions
Varies between species (2% to 5% per year for large mammals)
In nature, biotic potential is rarely reached

26.4 Limiting Factors
Any essential resource that is in short supply
All limiting factors acting on a population dictate sustainable population size
Carrying Capacity (K)
Maximum number of individuals that can be sustained in a particular habitat
Logistic growth occurs when population size is limited by carrying capacity
S-shaped curve
Logistic Growth
As the size of the population reaches carrying capacity, rate of reproduction decreases
When the population reaches carrying capacity, population growth ceases
Overshooting Capacity
Population may temporarily increase above carrying capacity
Overshoot is usually followed by a crash; dramatic increase in deaths
Density-Dependent Controls
Limiting factors become more intense as population size increases
Disease, competition, parasites, toxic effects of waste products
Density-Independent Controls
Factors unaffected by population density
Natural disasters affect large and small populations alike

26.5 Life History Patterns
Patterns of timing of reproduction and survivorship
Vary among species
Summarized in life tables and survivorship curves
Life Table
Tracks age-specific patterns
Population is divided into age categories
Birth rates and mortality risks are calculated for each age category
Life Table for Humans
Survivorship Curves
Graph of age-specific survivorship
Type I large mammals
Type II birds, lizards, small mammals
Type III invertebrates, fishes, plants, fungi
Read 26.6 Excellent example of directional selection

26.7 Human Population Growth
Population now 6.5 billion
Rates of increase vary among countries
Average annual increase is 1.3 %
Population continues to increase exponentially
Side-Stepping Controls
Expanded into new habitats
Agriculture increased carrying capacity; use of fossil fuels aided increase
Hygiene and medicine lessened effects of density-dependent controls
Future Growth
Exponential growth cannot continue forever
Breakthroughs in technology may further increase carrying capacity
Eventually, density-dependent factors will slow growth
Population Growth Curve
Population growth affects quality of life
Resource depletion
Competition for services
Increased pollution

26.8 Fertility Rates and Age Structure
Total fertility rate (TFR) is average number of children born to a woman
Highest in developing countries, lowest in developed countries
Fertility Rates Compared
Age Structure Diagrams
Show age distribution of a population
Age Structure Diagrams: 1997
Population Momentum
Lowering fertility rates cannot immediately slow population growth rate
Why? There are already many future parents alive
If every couple had only two children, a population would take 60 years to reach ZPG
Slowing Growth in China
World’s most extensive family planning program
Government rewards small family size, penalizes larger families, provides free birth control, abortion, sterilization
Since 1972, TFR down to 1.8 from 5.7
Effects of Economics
When individuals are economically secure, they are under less pressure to have large families

26.9 Demographic Transition Model
Postulates that as countries become industrialized, first death rates drop, then birth rates drop
Demographic Transition Model
Resource Consumption
United States has 5 % of the world’s population
Uses 25 % of the world’s minerals and energy
Per capita, Americans consume more resources and create more pollution than citizens of less developed nations
Projecting Human Population Size

Community Structure and Biodiversity
Chapter 27
27.1 Community
All the populations of species that live together in a habitat
Habitat is the type of place where a species normally lives
Habitat type shapes a community’s structure
Factors Shaping Community Structure
Climate and topography
Types of foods and resources available
Adaptations of species in community
Species interactions
Arrival and disappearance of species
Physical disturbances
Niche—way of life
Sum of activities and interactions in which a species engages to secure and use resources necessary for survival and reproduction
Fundamental vs. Realized Niches
Fundamental niche
Theoretical niche occupied in the absence of any competing species
Realized niche
Niche a species actually occupies
Realized niche is some fraction of the fundamental niche
Species Interactions
Most interactions are neutral; have no effect on either species (0/0)
Commensalism helps one species and has no effect on the other (+/0)
Mutualism helps both species (+/+)
Species Interactions
Interspecific competition has a negative effect on both species (-/-)
Predation and parasitism both benefit one species at a cost to another (+/-)
Close association of two or more species during part or all of the life cycle
Commensalism, mutualism, competition, predation, and parasitism are all forms of symbiosis

27.2 Mutualism (+/+)
Both species benefit
Many examples in nature
Some mutualisms are obligatory; partners depend upon each other
Obligatory mutualism between fungi and algae
Fungus supplies anchorage and water retention
Alga supplies photosynthate
Obligatory mutualism between fungus and plant root
Fungus supplies mineral ions to root
Root supplies sugars to fungus
Yucca and Yucca Moth
Obligatory mutualism
Each species of yucca is pollinated by only one species of moth
Moth larvae can grow only in that one species of yucca

27.3 Competition (-/-)
Interspecific - between species
Intraspecific - between members of the same species
Intraspecific competition is most intense
Competitive Exclusion
When two species compete for identical resources, one will be more successful and will eventually eliminate the other
Competitive Exclusion Expt
Resource Partitioning
Apparent competitors may actually have slightly different niches
Species may use resources in a different way or time
Minimizes competition and allows coexistence

27.4 Predation (+/-)
Predators are animals that feed on other living organisms
Predators are free-living; they do not take up residence on their prey
Natural selection promotes traits that help prey escape predation
It also promotes traits that make predators more successful
“Arms race” between predators and prey
Predator and Prey Populations are related
Multi-level interactions

27.5 Evolutionary Arms Race
Warning coloration

Predator Responses
Any adaptation that protects prey may select for predators that can overcome that adaptation
Predator adaptations include stealth, camouflage, and ways to avoid chemical repellents

27.6 Parasitism (+/-)
Parasites drain nutrients from their hosts and live on or in their bodies
Natural selection favors parasites that do not kill their host too quickly
Biological Controls
Parasites are commercially raised and released in target areas as biological controls
An alternative to pesticides
Must be carefully managed to avoid upsetting natural balances
27.7 Skip

27.8 & 27.9 Succession
Change in the composition of species over time
Pioneer Species
Species that colonize
barren habitats
Annual plants
Grow well in sunny and dry conditions
Have many offspring, opportunistic, “weedy”
Improve conditions for other species that replace them (N-fixing)
Climax Community
Stable array of species that persists relatively unchanged over time
Succession does not always move predictably toward a specific climax community; multiple stable communities are possible
Keystone Species
A species that can dictate community structure
Removal of a keystone species can cause drastic changes in a community; can increase or decrease diversity

27.10 Exotic Species
Species that has become established outside of its natural home range
Becomes part of a new community
Exotic Species Introductions
Introduction of a non-indigenous (non-native) species can be accidental or intentional
Have no natural enemies or controls
Can outcompete native species
Kudzu in SE United States
Tree-of-heaven in Turlock

27.11 Biodiversity
The sum of all species occupying a specified area during a specified interval
Patterns of Diversity:Latitude
Diversity of most groups is greatest in tropics; declines toward poles
a) ants
b) birds
Why are the Tropicsspecies rich?
More sunshine, more rain, longer growing season--resources are plentiful and reliable
Tropical species have been evolving for a longer period of time than temperate species
Species diversity is self-reinforcing

27.12 Endangered Species
A species that is extremely vulnerable to extinction
Habitat loss is the major cause of species endangerment and extinction
Endangered Species Recovery Program at CSU Stanislaus
San Joaquin kit fox, Riparian brush rabbit, California jewelweed, Kern mallow
Indicator Species
Types of species that may warn of impending loss of biodiversity
Birds, amphibians

27.13Conservation Biology
Study of biological diversity
Methods of preserving biodiversity
Ways to utilize biodiversity sustainably

27.13 Preserving Biodiversity
Requires identifying and protecting regions that support the highest levels of biodiversity
It is possible to protect a habitat and still withdraw resources in a sustainable way
Areas at Risk

Chapter 28
28.1 Ecosystem
An association of organisms and their physical environment, interconnected by a flow of energy and a cycling of raw materials
Modes of Nutrition
Capture sunlight or chemical energy
Extract energy from other organisms or organic wastes
Simple Ecosystem Model
Trophic Levels
Food Chain
A straight line sequence of who eats whom
Simple food chains are rare in nature
Food Web

28.2 & 28.4 Energy Losses
Energy transfers are never 100 percent efficient
Some energy is lost at each step
Limits the number of trophic levels in an ecosystem
Biomass Pyramid
Energy Pyramid
Primary producers trap about 1% of the solar energy that enters an ecosystem
Only ~10% is passed on to next level
All Heat in the End
At each trophic level, the bulk of the energy received from the previous level is used in metabolism
This energy is released as heat energy and lost to the ecosystem

28.3 Biological Magnification
A nondegradable or slowly degradable substance becomes more and more concentrated in the tissues of organisms at higher trophic levels of a food web
Ex: DDT and Mercury
DDT in Food Webs
Synthetic pesticide used in the US before the 1970s
Birds that were top carnivores accumulated DDT in their tissues
A side effect of DDT is brittle egg shells
Rachel Carson
Author of “Silent Spring” (1962)
Awakened public interest in limiting the use of pesticides

28.5 Biogeochemical Cycles
The movement of an element from the environment to living organisms and back to the environment
Main reservoir for the element is in the environment

28.6 Water Cycle
Any region where precipitation flows into a single stream or river.
Ex: Mississippi, Amazon, San Joaquin
Underground layer of rock that contains water (groundwater)
Aquifer Depletion
A build up of salt in the soil as irrigation water evaporates
Can stunt plant growth and decrease crop yields

28.7 Carbon Cycle
Carbon moves through the atmosphere and food webs on its way to and from the ocean, sediments, and rocks
Sediments and rocks are the main reservoir
Carbon Cycle
Carbon in Atmosphere
Carbon dioxide is added to atmosphere
Aerobic respiration, volcanic action, burning fossil fuels
Removed by photosynthesis—plant a tree.

28.8 Greenhouse Effect
Greenhouse gases impede the escape of heat from Earth’s surface
Ex: Carbon dioxide, CFCs, methane, nitrous oxide
Carbon Dioxide Increase
Carbon dioxide levels fluctuate seasonally
The average level is steadily increasing
Burning of fossil fuels and deforestation are contributing to the increase
Other Greenhouse Gases
CFCs - synthetic gases used in plastics and in refrigeration
Methane - produced by termites, bacteria, and livestock
Nitrous oxide - released by bacteria, fertilizers, and animal wastes
Greenhouse Gases
Global Warming
Long-term increase in the temperature of Earth’s lower atmosphere
Effects of Global Warming
As polar ice and glaciers melt, sea levels rise
Effects of hurricanes and storms worsen
Evaporation rates increase causing climate change (floods and droughts)

28.9 Nitrogen Cycle
Nitrogen important to form amino acids and nucleotides
Main reservoir is nitrogen gas in the atmosphere (N2)
N2 can’t be used directly by plants
Nitrogen must first be fixed into useable forms
Nitrogen Fixation
Volcanic action, lightning, and nitrogen-fixing bacteria convert nitrogen gas into ammonia (NH3)
N2 NH3
Nitrogen Cycle
Human Effects
Humans increase rate of nitrogen loss by clearing forests and grasslands
Humans increase nitrogen in water and air by using fertilizers and by burning fossil fuels
Resulting nitrogen oxides are air pollutants that cause acid rain.

28.10 Phosphorus Cycle
Phosphorus is part of phospholipids and all nucleotides
Often a limiting factor in ecosystems
Main reservoir is Earth’s crust; no gaseous phase
Phosphorus Cycle
Human Effects
In tropical countries, clearing lands for agriculture may deplete phosphorus-poor soils
In developed countries, phosphorus runoff is causing eutrophication (nutrient-enrichment) of waterways

29.2 Air pollution in the San Joaquin Valley
Air pollution
substance that has accumulated in harmful or distruptive amounts
Air Pollutants
Carbon oxides
Sulfur oxides
Nitrogen oxides (NOx)
Volatile organic compounds (VOCs)
Particulate Matter (PM)
Particulate Matter (PM)
PM2.5 and PM10 based on the particle diameter (µm)
May be directly emitted as dust or soot
May form in the atmosphere from other compounds
Particulate Matter
Problematic in winter
Worst at night or in early mornings
Woodburning stoves and fireplaces
In the winter up to 30% of the PM in the valley comes from woodburning.
A natural gas fireplace is 300x less polluting than wood.
Not directly emitted
Forms when industrial and vehicular emissions (especially NOx and VOCs) react in sunlight
Problematic in the summer
Worst in the afternoon and evening
Carpool, bus, or bike to work/school
Use electric lawn mowers and tools
Use gas grills instead of briquettes
Choose non-motorized recreation
Health impacts of PM and Ozone in one year
460 premature deaths
260 hospital admissions
23,300 asthma attacks
325 new cases of chronic bronchitis
3,230 cases of acute bronchitis in children
17,000+ days of respiratory symptoms in children
188,400 days of reduced activity in adults
Economic Impacts
Air pollution costs the valley
$3 billion/yr. ($1,000/person/yr.)
In addition to health impacts…
188,000 days of school absences
3,000 lost work days
Jane V. Hall et al. (2006)
CSU Fullerton
Valley’s poor air quality
Many factors contribute:

How bad is it?
Air Quality Index
Which cities have the worst air in CA?
Compared to the SJ Valley:
Los Angeles area produces 10x the air pollution per square mile.
LA’s air is only slightly worse than ours.
Compared to the SJ Valley:
Bay area produces 6x the air pollution per square mile.
Bay area’s air quality is much better than ours.
Good news (1990-2005)
Attainment of federal standards for PM10
Reduced by 13%
Improvement in PM2.5 levels
Reduced by 10%
Improvement in ozone levels
82% reduction in the number of days violating the standard
21% reduction in the peak concentration
So what can we do?

Biology1010:Origin and Early Evolution of Life on Earth
Some key words, phrases, and ideas :

science vs pseudoscience vs not science
natural forces vs supernatural forces
species--definitions and Latin bionomials
Lamarckian evolution vs Darwinian evolution
Oparin-Haldane model; Urey-Miller experiment
RNA/protein-based metabolism
Eubacteria vs Archaea vs proto-Eucarya
chemoheterotrophy vs chemoautotrophy vs photoautotrophy
fermentation vs anaerobic respiration vs aerobic respiration; membrane-bound electron transport chains
anoxygenic photosynthesis vs oxygenic photosynthesis

basic questions for the course
What is a species?
How many species are there?
Where did they all come from?
How do they interact with each other and with the environment?
early approaches
Plato and Aristotle--ideals, the scalae naturae, and special creation
Linnaeus--Latin binomials, heirarchy based on structural relationships
New questions: What do these relationships mean? What are fossils and what does the fossil record mean
de Buffon--centers of creation; still not scientific and does not explain fossil
scientific approaches
What is science? How is the scientific approach different from other approaches?
Hutton and Lyell and the age of the Earth
Lamarck and the theory of evolution by acquired characteristics
based on the changes seen in the fossil record of a certain group of snails
basic mechanism:
individuals develop needed traits, lose unnecessary or unused traits
changes made in parents are passed along to offspring
rejected at first because the idea of evolution was not accepted, later because no known force to account for the development of needed structures in a way that can be inherited by offspring (note: many educated people believe in Lamarckism without realizing it)
Darwin used his own observations of relatedness, plus Hutton''s and Lyell''s interpretation of the geologic record, plus Malthus''s ideas concerning the growth of populations to develop a theory of evolution by means of natural selection
basic mechanism
more offspring are born than will reached maturity--losses caused either by limited resources or by predation (superfecundity and the struggle for existence)
while on average offspring are the same as their parents, there is a great deal of genetic variability within a family or species (individual variation and heredity)
some of that genetic variability gives organisms a better chance to reproduce (better competitors or better at avoiding predators or something along those lines)
a greater proportion of the next generation is born of parents with the "good'' variation, with a better chance at surviving and reproducing so that adaptive traits tend to accumulate within a population
tests of the theory
the fossil record supports the idea of evolutionary change
comparative anatomy (homologous structures) indicates relationships among existing organisms
comparative embryology indicates relationships among organisms
comparative mlecular biology indicates relationships among organisms
Haldane and others provided the means to test evolution on the microscale
new problem: What is the source of genetic variation?
initially much confusion between genetic and acquired variability and about how the variability is passed on
Mendel''s work with pea plants helped, but was ahead of its time; needed evidence from microscopy to support his views
Griffith discovered that traits could be passed from bacterium to bacterium (even if dead), implying that traits are carried by particular chemicals; Avery demonstrated that the chemical involved was DNA; Watson and Crick showed how DNA could work as genetic material; we are now able to manipulate DNA to create new variants
Earth''s earliest biosphere
sources of information
structure of the solar system, composition of meteorites
geologic history of Earth (times based on layering in sedimentary rocks and radioisotope dating of the rock material)
Hadean (4,500 mya to 3,800 mya) -- formation of the Earth, solidification of the crust
Archean (3,800 mya to 2,400 mya) -- beginnings of life on Earth
Proterozoic (2,400 mya to 550 mya) -- rise of oxygen in the atmosphere, advanced unicellular life on Earth
Paleozoic (550 mya to 245 mya) -- early development of multicellular life
Cambrian (to about 500 mya)
Ordovician (to about 440 mya)
Silurian (to about 410 mya)
Devonian (to about 360 mya)
Carboniferous (to about 290 mya)
Permian (to about 245 mya)
Mesozoic (245 mya to 65 mya)
Triassic (to about 210 mya)
Jurassic (to about 140 mya)
Cretaceous (to about 65 mya)
Cenozoic (65 mya to present)
Tertiary (to about 2 mya)
Quaternary (to recent times)
the biological record: fossils, comparative anatomy and development, comparative molecular biology
DNA-DNA hydridization
gene sequencing
origin of the Earth (Hadean period)
orgins of life on Earth
What constitutes life on Earth?
basic features of all life: organization, series of chemical reactions (metabolism), reproduction and growth (genetic machinery), responsiveness and homeostasis
features of life on Earth: cellular structure, genetic material consisting of double-stranded DNA, metabolic machinery involving proteins and RNA
How did life begin on Earth?
early conditions: atmosphere of CO2, N2, H2O, some NH3 and CH4, no O2; the lack of free oxygen may have been crucial
build-up of organic molecules led to the formation of a fiarly concentrated primordial soup
according to the Oparin-Haldane model, chemical reactions in the atmosphere caused the formation of the more complex molecules (sugars, amino acids); Urey-Miller experiment demonstrated the possibility of forming such molecules in simple systems
others, citing problems with the gas mixtures in the Urey-Miller experiment, suggest that precursors molecules were made in deep-sea systems similar to vents in existence today
still others contend that the precursors were formed in deep space and came to Earth in comets and meteorites
molecules in the primordial soup spontaneously formed more complex structures (proteinoids?, coacervate droplets?)
self-replicating structures formed
nucleic acids?
a quick review of nucleic acids
an RNA world?
can self-replicate in test-tube
can function as organic catalyst
somehow became the template for protein production (message, ribosomes, transfer system for amino acids)
somehow, the complex structures and the self-regulating structures formed a living structure
boundary (this is where proteinoids and droplets come in)
metabolic machinery involving enzymes whose formation is directed by RNA
energy storage in ATP
genetic system to pass information along to the next generation
Could this process have been repeated (started) elsewhere in the Solar System?
Venus -- probably too hot now and before, closer to the Sun and with a thick CO2 atmosphere
Mars -- now too cold and dry, lacking an atmosphere; in the past more similar to Earth so possible; some claim structures found in a meteorite (AH 84001) thought to have originated on Mars are fossils
Jupiter, Saturn, and the other gas giants -- no surface, no liquid water
moons of the gas giants
Europa (Jupiter)
Titan (Saturn)
life in the Archean
hypothesized structure of early cells
cell membrane of phospholipids and proteins
DNA-based genetics
protein synthesis using ribosomes, tRNA (genetic code)
chemoheterotrophic metabolism (fermentation)
division into distinct lineages (domains of life)
features and evolution of life in the Archean using Eubacteria as an example
cell structure
genetic material packaged into a nucleoid (bundled DNA)
metabolic machinery based on proteins and RNA (more or less standard; slight differences between eubacterial systems and systems in other domains are the basis of selective antibiotics )
cell membrane of phospholipids and proteins (more or less standard)
some have complex internal membrane systems to help compartmentalize photosynthesis
most have an outer wall containing the peptidoglycan (rigid material of sugar and small proteins)
Gram-positive vs Gram-negative walls
functions of walls
important metabolic features (in the context of the evolution of life)
anaerobic vs aerobic
chemoheterotroph vs chemoautotroph vs photoautotroph
electron-transport chains
fermentative vs respiratory heterotrophs
non-oxygenic vs oxygenic photoautotrophs
nitrogen fixation
importance of bacteria in human affairs
sewage treatment
primary treatment
secondary treatment: sludge digestors/bioreactors; BOD reduction
tertiary treatment
toxic waste clean-up
nutrient cycling
bacteria-induced redox reactions change solubility of metal ions
iron and manganese nodules
chemical and food production
disease agents
types of disease
infectious vs non-infectious; contagious
viral vs bacterial vs eukaryotic
symptoms vs disease
Koch''s postulates
if the putative pathogen is present in all hosts with the disease; and
if it can be isolated and cultured; and
if it causes the disease when introduced into a healthy host; and
it can be reisolated from the now infected host after the disease develeps
then the organism is probably the cause of the disease
evolution of bacteria
sources of variation
hypothesized pattern of evolution
anaerobic respiration (electron-transport chains)
anoxygenic photoautotrophy -- purple-sulfur bacteria and others
oxygenic photoautotrophy (chlorophyll-based photosynthesis) -- cyanobacteria
evolution of oxygenic photosynthesis -- the end of the Archean

Experimental Biology BSC 3402L
Table of Contents

Chapter 1 Introduction to Experimental Biology 4
Chapter 2 What is Science? 5
Chapter 3 Plant Reproductive Biology 9
Chapter 4 Pollen Vectors and Pollination Syndromes 16
Chapter 5 Foraging Ecology of Pollinators 26
Chapter 6 Experimental Design and Data 31
Chapter 7 Statistics--Distributions and Differences Between Means 37
Chapter 8 Statistics--Measures of Association 44
Chapter 9 Using the Library and Biological Literature 51
Chapter 10 Scientific Communication Proposals 55
Chapter 11 Scientific Communication Papers and Presentations 60
Chapter 12 Lab Exercise - Floral Morphology and Pollination Systems 65
Chapter 13 Lab Exercise - Costs and Benefits of Foraging 71
Chapter 14 Selected References on Pollination Ecology 77
Appendix 1 Hazards of the Wild 81
Appendix 2 Statement of Voluntary Consent
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