Sbi4uap - Workbook 1 - 2022-23 (182 Pages)

Trinity College School
Grade 12
AP Biology
Teacher: Dr. Pontieri (2022-23)
Unit 1 – Biochemistry
Unit 2 – Metabolism
Unit 5 – Evolution
BOOK #1 NAME: ___________________

SBI4UAP | Unit 1
Chemistry Fundamentals & Macromolecules
BIOCHEMISTRY
Learning Objectives: In this unit, you will learn…

1) The structure and properties of atoms related to radioactivity.
2) The structure/properties of molecules, including intramolecular bonding & solubility.
3) The three-dimensional shape of molecules and intermolecular attractions.
4) The properties of water and how they relate to biological phenomena.
5) The role of acids and bases in biology, including the importance of buffers.
6) The structure hydrocarbons, as well as isomers and properties tied to functional groups.
7) The structure and function of macromolecule classes (carbohydrates, lipids and proteins).
8) The chemical reactions of functional groups that create macromolecules.
9) The modelling of molecules in 3-D to understand the structure-function relationship.
10) The signal transduction pathways in effecting hormone-based cellular responses.
Name: _____________________ Teacher: ______________

1
Lesson ● Geometric Isomers Molecular Drawings Practice Problems
Unit 1 - Biochemistry Outline 8 ● Optical Isomers Isomers Practice Problems
Activity – Biomolecules in 3-D
TOPIC 1.1 | RADIOISOTOPES Homework & Assessments
Lesson ● Functional Groups Functional Groups Practice Problems
Lesson ● Course Welcome “Getting to Know You” Google Form 9
1 ● Trace Elements Contracts (Lab Safety & Academic Integrity) Activity – Biomolecules in 3-D
***Buffer Lab is DUE!
Demo – Extracting Iron from Cereal
TOPIC 1.6 | MACROMOLECULES Homework & Assessments
Lesson ● Radioisotopes
Lesson ● Dehydration & Hydrolysis Reactions Carbohydrate Review Questions
2 ● Types of Radiation
10 ● Carbohydrates - Monosaccharides
● Half-lives
● Biologically Useful Radioisotopes ● Carbohydrates - Disaccharides
***FOR QUIZ: Functional Groups

TOPIC 1.2 | CHEMICAL BONDING Homework & Assessments
Activity – Macromolecule Building
Lesson ● Ionic vs. Covalent Bonds EdPuzzle “Carbon”
3 ● Electronegativity Lesson
Inter/Intramolecular Forces Review
● Molecular Shape (VSEPR) 11 “OF” Test – Chemistry Basics, Water Chemistry & Organic Chemistry (mid-unit test)
● Molecular Polarity
● Intermolecular Bonding Lesson ● Carbohydrates - Polysaccharides Carbohydrate Review Questions
12 ● Lipids - Fats, Phospholipids, Steroids
Activity – Molecule Building Lipid Review Questions
TOPIC 1.3 | WATER PROPERTIES Homework & Assessments Activity – Macromolecule Building
Lesson ● Adhesion & Cohesion Water Chemistry Practice Problems Lesson ● Proteins - General Structure Protein Review Questions
4 ● High Heat of Vaporization & Capacity 13 ● Proteins - Structure Levels
● Highest Density at 4C
● Solubility & Transmission Demo – Protein Folding
Activity – Macromolecule Building
Demo – Water Properties
Lesson ● Protein Folding
TOPIC 1.4 | ACID-BASE CHEMISTRY Homework & Assessments 14 ● Protein Sorting ***PROBLEM SET Proteins (“of learning”)
Lesson ***FOR QUIZ: Chemistry Fundamentals Buffer Lab Check-in #1: Activity – Name that Molecule
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Complete Q1 (graphs)
Lab – Role of Buffers & pH
TOPIC 1.6 | CELL COMMUNICATION Homework & Assessments
Lesson ● Acids & Bases Buffer Lab Check-in #2: Lesson ● Tyes of Receptors *** Problem Set Assignment is DUE!
6 ● Neutralization Reactions 15 ● Signalling Pathways
Complete Q2-6
● Conjugate Acids & Bases ● Downstream Response
● Buffers
Activity – Modelling Cell Communication
TOPIC 1.5 | ORGANIC CHEMISTRY Homework & Assessments Lesson
Lesson ● Organic Chemistry Introduction Buffer Lab Check-in #3: 16 “OF” Test – Biochemistry (final cumulative unit test)
7 ● Types of Hydrocarbons Complete Q7-9
● Structural Isomers
***FOR QUIZ: Water & Acid-Base Chemistry
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1.1 RADIOISOTOPES
ISOTOPE = Two atoms of the same element that differ in the number of neutrons.
Atomic number = # of protons
Mass number = # protons + # neutrons
Naturally Occurring Isotopes of Carbon

Carbon Atomic Mass Number of Relative Structural
Isotope Number Number Neutrons Abundance Stability
C-12 98.9% Stable
C-13 1.1% Stable
C-14 trace Radioactive
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RADIOISOTOPE = Unstable isotope that emits radiation.
RADIATION = Emission of tiny, energetic, invisible particles by the nuclei of unstable atoms.
Three Main Types of Radiation

IONIZING PENETRATING
TYPE GREEK DESCRIPTION POWER POWER
SYMBOL
(rank low, intermediate, high)
ALPHA
Unstable nucleus emits an alpha particle

composed of 2 protons and 2 neutrons.
The alpha particle picks up two electrons from its
surroundings to become a free helium atom.
BETA
Unstable nucleus emits an electron (beta particle).

As the emission occurs, a neutron turns into a proton.
GAMMA
When an unstable nucleus emits high-energy

electromagnetic radiation (the radiation has no mass,
and so its emission does not change the element).
Gamma often accompanies alpha & beta emission.
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HALF-LIFE = Time required for half of a radioactive sample to decay.
The half-life is constant, but is different for each

isotope.
Parent isotope undergoes decay, while the

daughter isotope is the decay product.
Sample Problem!
If a patient is administered 10 ng of technetium-99m,
how much will remain one day later, assuming that
no technetium has been eliminated by any other
process? The half-life of technetium-99m is 6 hours.
(Hint: you don’t need an equation to solve this!)
Examples of Useful Radioisotopes in Biology

APPLICATION ISOTOPE HALF-LIFE RADIATION EMITTED
(give specific isotope) (time period) (alpha, beta, gamma?)
A Used in archeological dating.
B Used in thyroid therapy.
C Used in nuclear reactors.
D Used in geological dating.
E Used in brain scans.
F Used in cancer therapy.
G Food irradiation.
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1.2 CHEMICAL BONDING
The chemical behaviour of an atom depends mostly on the number of
electrons in its outermost shell, the valence shell.
Atoms with incomplete valence shells interact by either sharing or

transferring valence electrons, thereby forming chemical bonds.
Two types of INTRAMOLECULAR forces:
BOND DESCRIPTION
Ionic Forms between a metal & non-metal and involve electron transfer such as NaCl.
Covalent Form between two non-metals and involves electron sharing such as H2O.
ELECTRONEGATIVITY = Attraction of an atom for the electrons of a covalent bond.
Table of
Electronegativity
Values
If electrons in a covalent bond are not shared equally, this is a POLAR covalent bond.
If electrons in a covalent bond are shared equally, this is a NON-POLAR covalent bond.
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Sample Problem! Determine if HCl is an ionic or covalent molecule using electronegativity
values. Then, sketch the molecule and indicate if bonds are polar or non-polar (if covalent).
Where are Electrons Located?

While electrons are often visualized as concentric paths, like planets orbiting the sun, in reality,
an electron occupies a more complex 3-D space.
ORBITAL
A 3-D space with a
high probability of
finding an electron.
A maximum of 2
electrons are found
in each orbital.
An example using
neon shown in the
diagram.
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Molecular Shape
The shape of a molecule is determined by the arrangement of electron
orbitals shared by the atoms involved in the bond.
The shape of a molecule is determined by the

arrangement of electron orbitals shared by the
atoms involved in the bond.
For atoms with electrons in both s and p

orbitals, the formation of a covalent bond leads
to the hybridization of the orbitals to four new
orbitals in a tetrahedron shape, the most
common shape seen in biological molecules.
VSEPR THEORY stands for “Valence Shell Electron Pair Repulsion”

1) lone pair-lone pair electron repulsion
Used for predicting the shape of molecules
2) lone pair-bonding pair electron repulsion
and takes into account 3 things:
3) bonding pair-bonding pair electron repulsion
Sample Problem: Build the following molecules and sketch their shape. Include partial
charges and lone pairs in your drawing. Determine whether the molecule is polar or nonpolar.
a) H2O b) CH4
c) CH3Cl d) CCl4
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INTERMOLECULAR BONDS: Interactions Between Molecules
While intermolecular bonds are weak, collectively they have strength.
Two types of INTERMOLECULAR forces:
Bond Forms Relative Example – sketch it!

Type between… Strength
Weak, but Two molecules of HCl

Dipole Form between stronger
two than
___________ London
molecules. forces.
Weaker Two molecules of Cl2

Form between than
London two dipole
___________ forces.
molecules.
Sample Problem: Draw the interaction of ammonia (NH3) and water showing all partial
charges and possible lone pairs for each molecule. Draw the interaction if any using a
dashed line. Indicate which intermolecular force is involved.
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Intramolecular & Intermolecular Forces Practice Problems
1. For the following molecules:
a) Draw the structures using the correct molecular geometry.
b) Show lone pairs, if present.
c) Determine whether the intramolecular bonds are polar or nonpolar.
d) Label partial charges, if present.
e) State whether the molecule is polar or non-polar.
f) Classify the molecular shape of the molecule.
a) H2S b) CCl4
Molecular Shape: Molecular Shape:
c) CH4 d) CO2
Molecular Shape: Molecular Shape:
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2. Which of the following pairs of compounds can form H-bonds? For those that can, mark the
position of the partial charges in the molecules and indicate where the H-bonds will form. For those
that can’t form H-bonds, describe whether the IMF is ionic, dipole or London Dispersion Forces
(LDF).
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1.3 WATER PROPERTIES
● Water is a polar molecule.
● It can form hydrogen bonds with up to four water neighbors.
● Hydrogen bonds can form, break, and reform with great frequency.
● Its hydrogen bonds account for its unique properties.
Draw a molecule of water hydrogen-bonded to four other water molecules:
Biologically Important Properties of Water
Characteristic Property Explanation Effect Example
Water clings COHESION Water molecules form High surface Water strider walks on
H-bonds with one tension surface of pond.
another.
Water forms droplets
(beads) on surface.
ADHESION Water molecules form Capillary Capillary action causes

H-bonds with other action water to creep up a
polar materials. narrow glass tube and
wick up paper.
Movement of fluids in
blood capillaries and plant
xylem vessels.
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Characteristic Property Explanation Effect Example
Water absorbs HIGH H-bonding causes Temperature Keeps constant body

lots of heat SPECIFIC water to absorb a large moderation temperature despite
HEAT amount of heat before fluctuations in external
CAPACITY its temperature temperature.
increases appreciably
& also causes it to lose Aquatic environments are
large amounts of heat thermally stable.
before its temperature
decreases significantly.
HIGH H-bonding causes Evaporative Sweating/panting to cool

SPECIFIC liquid water to absorb a cooling down in animals.
HEAT OF large amount of heat to
VAPORI- become a vapour. Transpiration to cool
ZATION down in plants.
Solid water is HIGHEST As water molecules Ice floats on Fish and other aquatic
less dense DENSITY cool below 0°C, they liquid water organisms are able to
than liquid 4°C form a crystalline survive in winter.
water lattice; the H-bonds
spread the molecules Floating ice also insulates
apart, reducing the the underlying water.
density below that of
liquid water.
OTHER IMPORTANT WATER PROPERTIES
LOW VISCOSITY
Water flow rates allow good speed to transfer materials such as blood and phloem sap.
COLOURLESS WITH HIGH TRANSMISSION OF LIGHT

Light penetrates tissues and aquatic environments, allowing underwater plants and protists to
photosynthesize and keep aquatic ecosystems healthy.
“VERSATILE SOLVENT”
Water is an effective solvent because it forms H-bonds with charged & polar covalent molecules.
HYDROPHILIC (“water-loving”): polar and ionic molecules are soluble in water.
HYDROPHOBIC (“water-fearing”): non-polar molecules are insoluble in water.
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Water Chemistry Practice Problems
1) Why is it erroneous to say that “water is the universal solvent”?
2) Hydrocarbons contain many hydrogen atoms but are not known to carry out hydrogen
bonding. Explain this apparent discrepancy.
3) Discuss the solubility of the following substances with water.

a) sugars d) octane
b) ethanol e) potassium chloride
c) carbon dioxide f) phospholipids
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4) For each, state the property of water and explain its biological importance:
a) clarity of seawater d) hands washed in water
b) water traveling up the xylem in plants e) ice forms on pond in winter
c) transport of glucose in bloodstream f) dog pants on a hot summer day
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1.4 ACIDS, BASES & BUFFERS
ACID: dissolved in water dissociates to form BASE: dissolved in water dissociates to form
H3O+(aq) ions in solution (otherwise known as H+) OH-(aq) ions in solution
Example: Example:
Neutralization Reaction: the reaction of an acid and a base to produce water and a salt
Example:
“Autoionization of Water” Although pure water is virtually 100% molecular, a small

number of water molecules do ionize. This is due to collisions occurring between H2O
molecules that transfer an H+ ion to the other H2O molecule according to the reaction:
The autoionization of water results in water having both acid and base properties and makes water
a very weak electrolyte and a poor conductor of electricity. The double arrow reaction symbol that
makes it an “equilibrium reaction” because forward and reverse reactions occur at same rate.
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Acid & Base Strength
Strong Weak
Completely ionize in solution. Partially ionize in solution.

Acid
Example: Example:
Completely ionize in solution. Partially ionize in solution.

Base
Example: Example:
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Conjugate Acids & Bases
Bronsted-Lowry Theory:
ACID = proton ___________
BASE = proton ___________
Example: Acetic acid solution, CH3COOH (aq)
BUFFER: Resist changes to pH even when H+ or OH- are added.

Consist of a weak acid and base conjugate pairs. Helps to maintain a set pH.
Example: Carbonic acid/bicarbonate buffer
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Acid-Base Chemistry Practice Problems
1) Identify the two conjugate acid-base pairs in the following acid-base equilibrium:
HCOOH (aq) + CN-(aq) < === > HCOO-(aq) + HCN(aq)
2) In each pair, identify the stronger acid or the stronger base (hint: use the chart!):
a) H20 or NH4+
b) NO3- or HS-
c) CO32- or PO43-
d) HC03- or HPO42-
3) For each of the following:

a) Write an equation for the reaction of each with water
b) Select the conjugate acid-base pairs for each reaction
i) HF (a weak acid)
ii) NH3 (a weak base)
iii) HBr (a weak acid)
iv) H2S (a weak acid)
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1.5 ORGANIC CHEMISTRY
Biologically important molecules (“macromolecules”) include:
o Carbohydrates: C, H, O
o Lipids: C, H, O
o Proteins: C, H, O, N
o Nucleic Acids: C, H, O, N, P
Why is carbon so versatile?
• Bonding capacity of 4
• Forms a tetrahedron
• Can form covalent bonds with itself and other elements (ex. H, N, O)
• Can form single, double and triple bonds with itself
• Can form large and complex molecules
Variation in Carbon Skeletons: Hydrocarbons vary with respect to…
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TYPES OF HYDROCARBONS
Alkanes
Formula: (CnH2n+2)
Bond between carbons:
End in:
Alkenes
Formula: (CnH2n)
End in:
Alkynes
Formula: (CnH2n-2)
End in:
Example Alkanes…
# carbons name # carbons name
1 6
2 7
3 8
4 9
5 10
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Molecular Drawings Practice Problems
There are different ways chemists depict molecules, especially the large molecules typically
seen in biology: ball-and-stick, Lewis structures and line drawings. Examples are shown.
1) Which types of drawings in Model 1 provide more accurate images of the shape of a
molecule? Justify your reasoning.
2) Symbols and atoms of what element(s) are missing from the line drawings? Suggest a
reason why this is.
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3) In reading a line drawing, how do you know where atoms of these elements are in the
structure if they are missing from the drawing?
4) Locate the carbon and hydrogen atoms in the line drawing of the amino acid isoleucine
shown below and draw them in as if the drawing were a Lewis structure.
5) Below is a diagram of retinol, the most common type of Vitamin A. Draw a line drawing
representation of this molecule
6) Isopropyl alcohol (C3H7OH) is a 3-carbon molecule with an –OH group attached to the
middle carbon. Draw this molecule using the Lewis structure and line structure diagrams.
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ISOMERS
ISOMERS = Compounds with the same molecular formula
but with different structures (hence different properties).
Structural
Isomers
Isomers that differ in the
covalent arrangements of
their atoms.
Geometric
Isomers
Isomers which share the
same covalent
partnerships, but differ in
their spatial arrangements.
Optical Isomers
(Enantiomers)
Isomers that are mirror
images of each other
occurring when 4 different
atoms or groups of atoms
are bonded to the same
carbon.
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HELP !!!
How do I Draw Structural Isomers?
Let's not write in H atoms so that we can focus on the carbon chain.
To make an isomer, break off an atom from the chain & stick it somewhere else within the chain.
Twisting, bending or flipping molecules doesn't turn them into different isomers.
That is,
So, there's no point in zigzagging or twisting. Just keep it straight!
Watch out for isomers that are the same by numbering the chain in both directions (left to right &
right to left) and choosing the numbering that has the side chain emerging at the lowest number.
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AN EXAMPLE...What are the isomer of C6H14?
Let's start with the straight chain.
Now reduce the chain by one carbon and add a side group.
BUT… 4-methyl pentane is not an isomer

because you must count from the side
that gives you the lowest #'s possible.
Finally, there are 2 more isomers when you further reduce the chain by one carbon.
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Isomers Practice Problems
1) Draw structural isomers for the following compounds – as many as you can find:
a) pentane (C5H12)
b) butanol (C4H9OH)
2) Classify each compound as a cis isomer, trans isomer or neither.
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3) Draw geometric isomers for these compounds, stating which are cis and trans forms:
a) 1,2-dichloroethene (C2H2Cl2)
b) but-2-ethene (CH3CHCHCH3)
4) Identify if the following are cis (with a circle) or trans (with a square) isomers. If the
compound is neither cis or trans, leave it blank.
5) Draw optical isomers of CHBrCH3OH. Name the isomers.
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FUNCTIONAL GROUPS ● Functional groups are the parts involved in reactions.
● Functional groups have constant properties.
Functional Class Structural Special Example

Group Formula Properties
Hydroxyl ALCOHOLS
—OH
ALDEHYDES
Carbonyl
—CHO
KETONES
Carboxyl CARBOXYLIC
—COOH ACIDS
Amino AMINES
—NH2
Phosphate ORGANIC
—OPO32- PHOSPHATE
Sulfhydryl THIOL
—SH
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Functional Groups Practice Problems
30
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Biological Macromolecules in 3-D
BLACK = Carbon (C)
WHITE = Hydrogen (H)
RED = Oxygen (O)
BLUE = Nitrogen (N)
YELLOW = Sulfur (S)
GREEN = Chlorine (Cl)
LONG, BENDY BONDS = Single bonds
SHORTER BONDS = Double bonds
PART A – ORGANIC MOLECULES
1. Build and sketch a molecule of ethane (C2H6). Describe the molecule’s structure and polarity:
❒ Shape: ___________________________________
❒ Charge symmetry: __________________________
❒ Polar or nonpolar: ___________________________
❒ Type of hydrocarbon: ________________________
2. Build and sketch a molecule of ethene (C2H4). Describe the molecule’s structure and polarity:
❒ Polar or nonpolar: ___________________________
❒ Type of hydrocarbon: ________________________
3. Build and sketch a molecule of dichloroethene (C2H2Cl2).
❒ Type of isomer created (cis or trans): ________________
❒ Polar or non-polar: _______________________________
❒ Category of isomer: _______________________________
4. Build and sketch a molecule of dichloroethene (C2H2Cl2).
❒ Type of isomer created (cis or trans): ________________
❒ Polar or non-polar: _______________________________
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5. Remove one Cl atom and attach to the carbon that already has a Cl attached. Sketch the
structure you have made.
❒ Type of isomer created: __________________________
6. Build and sketch a molecule of hexane (C6H14). Describe the molecule’s structure and polarity:
❒ Charge symmetry: _____________________
❒ Polar or nonpolar: ______________________
❒ Type of hydrocarbon: ___________________
7. Build and sketch as many structural isomers as possible for hexane.
8. Rebuild your unbranched hexane molecule and build a second one. Position them next to one
another. What types of intermolecular forces help hold hexane molecules together? Explain.
_______________________________________________________________________
PART B – FUNCTIONAL GROUPS

9. Build and sketch the following molecules. Circle and label the functional groups.
Ethanol (C2H5OH) is a volatile, flammable, colourless liquid. It

is a psychoactive drug and one of the oldest recreational drugs
best known as the type of alcohol found in alcoholic beverages.
❒ Soluble in water? ___________

❒ Acts as acid/base/neither? ___________
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Acetone (CH3)2CO is a volatile, flammable liquid found in nail polish
remover and paint thinner. It is naturally produced and disposed of
in the human body as a result of normal metabolism.

Formaldehyde (CH2O) solutions are used in embalming to

disinfect and temporarily preserve human and animal remains. It is
the ability of formaldehyde to fix the tissue that produces the
tell-tale firmness of flesh in an embalmed body. In post mortem
examinations a procedure known as the "sink test" involves placing
the lungs of an animal in an aqueous solution of formaldehyde; if
the lungs float it suggests the animal was probably breathing or
able to breathe at the time of death.

Methanethiol (CH3SH) is a colorless gas with a smell like rotten

cabbage! It is a natural substance found in the blood and brain and
is disposed of through animal feces. It occurs naturally in certain
foods, such as some nuts and cheese. It is one of the main culprits
of bad breath and smelly farts!

Formic acid (HCOOH) is present in stinging nettles, and is responsible

for the burning feeling on contact with them. It is also found in the
stings and bites of many insects, including bees and ants. When the ant
contracts its poison gland, the formic acid stored in this gland passes in
the sting and is propelled out in jets toward the attackers of the ant.
Since formic acid has a pH of ~2-3, the attackers usually flee, or are
killed. Because of its abundance in their diet, giant anteaters don’t
produced HCl for their gastric juice. Some birds are known to be
“addicted” to ant poison? They will often camp near an anthill and let
ants get trapped in their feathers so they can be squirted with formic
acid which protects birds from parasites.

Methylamine (CH3NH2) is a colourless gas derived from

ammonia. It has a strong odor similar to fish. Methylamines are
used to make intermediates for a wide range of agricultural
chemicals, including herbicides, fungicides and insecticides.

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10. Two organic molecules that will be discussed later in the course are shown below. Circle and label
all functional groups in these molecules.
SEROTONIN
GLYCERALDEHYDE-3-PHOSPHATE
B-ENDORPHIN
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COENZYME A
THYROID-RELEASING HORMONE
TETRACYCLINE
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For each of the following compounds:
a) Draw the structural formula for each of the following.
b) Circle and identify each functional group.
a) C5H11OH b) (C4H9)O(C3H7)
c) CH3CHO d) C3H7COOH
e) (C2H5)CO(CH3) f) (CHO)CH2(C2H5)
g) (NH2)2CHCH2CHO h) H2NCONH2 (urea)
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1.6 MACROMOLECULES
● Most macromolecules are polymers (exception: lipids).
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Reactions That Make and Break Molecules
DEHYDRATION (anabolic reactions) = Synthesize polymers (make bigger molecules)
HYDROLYSIS (catabolic reactions) = Digesting polymers (make smaller molecules)
Both dehydration and hydrolysis reactions need E N Z Y M E S !
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CARBOHYDRATES
❏ Organic compounds made C, H, and O in a ratio of 1:2:1 (eg. C=3, then C3H6O3).
❏ Three types of carbohydrates:
I. Monosaccharides
● Single sugars (eg. glucose, fructose, galactose).
● Are quick sources of energy.
● Can cross a cell membrane to get inside a cell.
GLUCOSE GALACTOSE FRUCTOSE
● Often monosaccharides are drawn in linear form, but in solution, form rings.
● Carbohydrates are highly soluble in water due to having many hydroxyl functional groups
and a carbonyl functional group (aldehyde = aldose sugar; ketone = ketose sugar).
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II. Disaccharides
● Double sugars (eg. maltose, sucrose, lactose).

● Formed by linking 2 monosaccharides by dehydration synthesis.
● Created via glycosidic (ether) linkages of monosaccharides (hydroxyl + hydroxyl).
● Examples of dissacharides:
❏ glucose + fructose = _______________ (sugar found in _________________)
❏ glucose + glucose = _______________ (sugar found in __________________)
❏ glucose + galactose = _______________ (sugar found in _________________)
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III. Polysaccharides
● Made up of many (100’s-1000’s sugar subunits).

● 2 important biological functions:
❏ Energy Storage
● glycogen (animal)
● starch (plant)
❏ Structural Support
● cellulose (plant cell walls)
● chitin (fungi cell walls, insect exoskeletons)
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Starch
● Helical glucose polymer in plants.
● Made of alpha glucose.
● Made of two molecules: amylose + amylopectin.
● Storage carbohydrate in potatoes, rice, flour.
● Easy to digest.
Glycogen
● Helical glucose polymer in animals.

● Found in liver and muscle cells, specifically in smooth ER.
● Made of alpha glucose.
● Highly branched, similar to amylopectin with more frequent branched.
● Easy to digest.
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Cellulose
● Linear unbranched polymer of glucose.
● Made of beta glucose.
● “Flip-flop” arrangement creates straight chains (not helical).
● Parallel strands form H-bonds together to make strong cable-like microfibrils.
● Microfibrils weave together to create the cell wall.
● Major component in plant cell walls.
● Difficult for carnivores to digest, so functions as ‘roughage’ to aid in digestion.
● Indigestible by humans, but digestible by some fungi, and other organisms such as cows or
termites with the help of microbes/archaeabacteria.
Chitin
● Polymer of an amino sugar (glucosamine) found in:
o exoskeletons of arthropods
o cell walls of fungus
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Carbohydrate Review Questions
1) Draw a ketotriose and an aldopentose sugar.
2) Demonstrate a reaction showing the synthesis of lactose. Label all reactants and
products. Circle and label functional groups, as well as the linkage created. Indicate the
type of reaction that this represents.
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3) Discuss features of cellulose molecules that account for both the strength and the water
absorbing qualities of paper towels? What property of water describes this phenomenon?
4) Discuss why can’t humans survive on a diet of grass like cows? Why is it good that
humans include vegetables in their diet despite the fact that they are not totally
digestible?
5) Glucose is the essential energy molecule of the cell. Explain how the protein called
GLUT-4 and the hormone INSULIN work to bring glucose from the blood into cells.
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LIPIDS
● Are one class of biological molecules that don’t include polymers.
● Formation: when glycerol and fatty acids join via an ester linkage (exception: steroids).
● Examples: waxes, certain pigments, fats, phospholipids and steroids.
● Properties: Mainly consist of non-polar hydrocarbons, thus are generally hydrophobic.
● Three types of lipids:
I. Fats
● 3-carbon glycerol (“head”) attached to 3 fatty
acids (“tails”, between 16-18 carbons in the tail).
● Aka triacylglycerols or triglycerides.
● Forms a hydrophobic molecule.
● Compact and light and thus

“efficient energy storage” (one
gram of fat stores more than twice
as much energy as one gram of
carbohydrate and does not attract
water for additional weight).
● Functions:
1) Energy storage
2) Cushions organs
3) Insulate body
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● Examples of fats include:
Saturated Fats (found in foods like butter, lard, animal fat trim )
● A naturally occurring fat derived from animal sources.
● Only single bonds between carbons of fatty acids (thus each C is fully “saturated” with H atoms).
● Solid at room temperature since fatty acids are straight and fit together closely.
Unsaturated Fats (found in foods like olive oil )

● A naturally occurring fat derived from plant sources.
● Contains a double bond between carbons of fatty acids (C atoms not fully saturated with H atoms).
● Liquid at room temp since fatty acids are kinked (at the double bond), not as compacted.
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II. Phospholipids
● Made up of a glycerol head attached to a phosphate group (making it the hydrophilic end)
that is attached to two fatty acid tails (making that end hydrophobic).
● “Two-legged” molecule similar to a fat, but with a polar, hydrophilic phosphate “head”
(substituted for 3rd fatty acid).
● Key molecule in formation of cell membranes when arranged in a “bilayer” form.
I. Steroids
● Four fused carbon rings.
● One type is cholesterol.
● Other types include

lipid-based hormones such as
testosterone and estrogen.
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Lipid Review Questions
1) A triglyceride molecule is shown below. Demonstrate what will happen to this molecule
in the presence of pancreatic lipase. Draw and label the chemical structures of all
reactants and products. State the type of chemical reaction that has occurred.
2) Compare the fundamental difference between a triglyceride and a phospholipid. Explain

how does this difference account for the hydrophobic and hydrophilic nature of the
phospholipids molecule?
3) Discuss the composition of the material on apples that makes them shiny and how it
relates to its function.
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4) Different groups of fatty acids are given below. Note: the “R” stands for the carboxyl group.
a) Draw the structures for each in the spaces.
i) R1 = -(C2H)2CH3 ii) R2 = -CH2CH3
iii) R3 = -C4H6CH3 iv) R4 = -(CH2)4CH3
b) Predict, with reason, which fatty acid stores the most energy?
5) Fat contains twice as many calories per unit weight as carbohydrate does. Explain why
fat has the advantage over carbohydrates for weight-efficient energy storage. How does
this compare to glycogen storage?
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PROTEINS
A very important group of molecules that have a variety of functions in cells:
1) Structural support – eg. keratin (fingernails), hair, bone, muscles, skin

2) Cell composition – eg. chromatin proteins, ribosomes, flagella
3) Transport – eg. hemoglobin
4) Signalling – eg. chemical messangers (hormones)
5) Biochemical reactions – eg. enzymes
Structure:
● Basic subunit = AMINO ACID
Functional Groups (no charges) Functional Groups (with charges)
● Proteins are large, unbranched molecules composed of 100’s-1000s of amino acids.
● Polypeptide = chain of amino acids that are linked together by peptide bonds.
● Like “beads on a string”.
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● The ribosome assembles amino acids into the polypeptide chain during protein synthesis.
● Peptide bonds (amide linkages) form following a dehydration reaction between an amine
and a carboxyl functional group.
● Given variation in the 20 amino acids, their combinations, lengths of polypeptide chains
and structural levels of assembly, proteins are the most diverse class of macromolecules.
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● R group – 20 possible side chains, which can be simple or more complex, non-polar,
polar, or electrically charged.
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● Protein shape is determined via 4 structure levels:
(a) PRIMARY STRUCTURE (b) SECONDARY STRUCTURE

(c) TERTIARY STRUCTURE (d) QUATERNARY STRUCTURE
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Primary Unique sequence of amino acids determined via inherited genetic information.
Structure
Even a slight change, such as one a.a. can change a protein’s shape thereby
making the protein non-functional (eg. sickle cell anemia).
Unfolded form of the protein.
Secondary Repeated coiling or folding due to regular H-bonds between amine and
Structure carboxyl functional groups along the polypeptide backbone.
Alpha helix – Spiral created due to H-bonds between every 4th amino acid.
Beta pleated sheet – Results when 2 or more polypeptide regions are parallel
to each other and thus can H-bond; these make the core of globular proteins
and dominate some fibrous proteins like a spider’s silk (teamwork of so many
H-bonds makes each silk fibre stronger than steel!).
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Tertiary Interactions between R groups that include:
Structure
Hydrophobic interactions – weak interactions between non-polar R groups
H bonds – weak interactions occurring between polar R groups
Ionic bonds – attraction between oppositely charged R groups
Disulfide bridges – strong interactions due to covalent bond forming between

sulphur atoms in the R groups of two cysteines
Quaternary Exists only in some proteins.

Structure Aggregates of 2 or more polypeptides.
Examples: hemoglobin, collagen, insulin.
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● Proteins may be fibrous (strand-like) or globular (blob-like):
● Proteins can be denatured – lose conformation and thus function due to changes in
temperature, salinity, pH, polarity of solvent…R-group bonds broken! Some proteins can
redenature (return to functional shape) but others can be permanently denatured.
● Folding of new polypeptides is often assisted by other proteins called chaperonins

(aka chaperone proteins).
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Protein Review Questions
1) Illustrate the appearance of alpha-helix and beta-pleated sheet regions of a polypeptide.
Describe the types forces involved in maintaining protein secondary structures. Discuss
whether alpha helix and beta-pleated sheet regions form R-group interactions with other
portions of the polypeptide chain.
2) Discuss evidence to support the claim that proteins are the most diverse class of
macromolecules.
3) Asparatame is an artificial non-saccharide sweetener formed between the amino acids

aspartic acid and phenylalanine. Demonstrate the reaction that produces Aspartame,
including all reactants and products. Give the name of the linkage created and state the
type of reaction involved.
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4) Shown below are the structures of 3 amino acids.
a) Rank these in order of water solubility and explain how you determined your answer.
b) Predict one amino acid that would be attracted to each of these amino acid R groups
and the type of intermolecular bond that will result.
Amino Acid #1 Amino Acid #2 Intermolecular Bond?
Phenylalanine
Threonine
Tyrosine
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macromolecule building activity
KEY:
Black = carbon
White = hydrogen
Red = oxygen
Blue = nitrogen
Short bonds = single bonds
Long bonds = double bonds
CARBOHYDRATES
1. Use the diagram below to form a straight chain glucose molecule. Use a piece of tape to
label carbon 1. Then rearrange the molecule so that you form the ring form for glucose.
2. Circle/label the functional groups found in both the straight chain and ring form for glucose.
a) What accounts for the high solubility of carbohydrates in water? _____________________
b) What intermolecular force dominates the interactions of carbohydrates and water? ______
3. Find another group with a ringed glucose. Orient the two α-glucose rings so that the hydroxyl
group on carbon-1 of one ring faces the hydroxyl group of carbon-4 on the other and create a
linkage between the two molecules.
a) What type of reaction is this? _________________________________
b) What is the name of the linkage that has been created? ________________________
c) What is the name of the resulting molecule? ___________________________
d) What is the other product that has been created in this reaction? _________________
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LIPIDS
4. Build a hexane molecule. Convert one of the terminal
methyl groups (-CH3) on each hexane molecule into a
carboxyl group (-COOH). Sketch your molecule.
Circle and label the functional groups.
a) Type of biomolecule created: _______________________________________________
b) Shape of hydrocarbon tail (straight or kinked): _________________________________
c) Meaning of “amphiphatic” molecule: __________________________________________
d) When in water, does this molecule act like an acid or base? _______________________
5. Create a double bond between carbons 3 and 4.

Sketch this molecule.
a) Number of hydrogens lost with double bond addition: __________
b) Type of fatty acid created by introduction of double bond: _______________________
c) Type of isomer created (cis or trans): _______________________________________
d) Shape of hydrocarbon tail (straight or kinked): ________________________________
e) Likely state at room temperature – liquid or solid? _____________________________
6. Build and sketch the other isomer with the second molecule.
a) Type of isomer created (cis or trans): ____________________________________
b) Shape of hydrocarbon tail (straight or kinked): _____________________________
c) Isomer most like a saturated fatty acid in shape (cis or trans): _________________
d) Likely state at room temperature – liquid or solid? _____________________
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7. Construct a molecule of glycerol (see diagram right). Circle and label all
functional groups. What is this molecule’s solubility in water like?
_______________________________________________________
8. Attach the two fatty acid molecules you created above to the glycerol.
a) Name of linkage created? _____________________________________________
b) If 3 fatty acids were attached, name of this molecule? ________________________
c) Would this molecule be hydrophilic, hydrophobic or both? _____________________
d) One carbon on the glycerol is free. What if this carbon was bonded to a phosphate group?
What is the specific type of biomolecule? _____________________________
PROTEINS
9. Construct the amino acids glycine and cysteine, using the diagrams.
a) On the diagrams given above, circle and label all the functional groups and R-groups.
b) Indicate the whether the R group is charged, polar or non-polar?
Glycine R group = ______________ Cysteine R group = ______________
10. Position the carboxyl end of one amino acid beside the amino end of the second amino acid.
Form a linkage between the two molecules.
a) What is the name of the linkage created? ___________________
b) Name the products formed: ______________ & ______________
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1.7 CELL COMMUNICATION
Reception Transduction Response

A chemical signal binds to a Binding leads to a change in the The transduced signal
cellular protein, typically at receptor that triggers a series of triggers a specific cellular
the cell’s surface. changes along a activity.
signal-transduction pathway.
STAGE 1: SIGNAL RECEPTION
Why can’t most signal molecules pass

through the plasma membrane?
Binding of the ligand and receptor leads to change in

the shape or the receptor or to aggregation of
receptors to trigger changes intracellularly.
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STAGE 2: SIGNAL-TRANSDUCTION PATHWAYS
▪ Signal transduction pathways allow for small amounts of a hormone to have LARGE EFFECTS.
▪ The original signal molecule is not passed along pathway, rather its information is passed on.
▪ Signal transduction pathways act like falling dominoes…
▪ Signal transduction pathways (STPs) coordinate and regulate key cellular processes through:
MULTISTEP PATHWAYS
The signal-activated receptor activates
another protein, which activates another
protein, and so on, which causes a large
cellular response.
SIGNAL AMPLIFICATION
At each step in a cascade, the number of
activated products is much greater than
in the preceding step.
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“Phosphorylation Cascade” - Many of the relay molecules in a STP are protein kinases that
lead to a “phosphorylation cascade”, and each protein phosphorylation leads to a shape change that
typically converts a protein from an inactive form to an active form.
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Second messengers participate in pathways initiated by both G-protein-linked and tyrosine-kinase
receptors, and the two most important are cyclic AMP and Ca2+:
Cyclic AMP (cAMP)

Binding by the signal to a receptor activates a
G protein that activates adenylyl cyclase
in the plasma membrane.
The cAMP from the adenylyl cyclase diffuses

through the cell and activates a serine/threonine
kinase, called protein kinase A that
phosphorylates
other proteins.
Calcium ions (Ca2+)
Cytosolic concentration of Ca2+ through the release of stores holding Ca2+ in the ER which activate
signaling pathways directly or bind to the protein calmodulin that can activate proteins.
Increased Ca2+ can cause muscle cells contraction, exocytosis and mitosis in animal cells, or trigger
responses such as drought in plants.
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STAGE 3: ACTIVATION OF CELL RESPONSE
▪ Ultimately, a signal-transduction pathway leads to two possible pathways:
1) ENZYME ACTIVATION
2) PROTEIN SYNTHESIS
▪ Different effects in different cells can lead to different responses to the same signal.
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ENZYME ACTIVITY
Example: Epinephrine (protein hormone)
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PROTEIN ACTIVITY
Example: Growth Factor (protein hormone)
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SBI4U | Unit 2
Enzymes & Cell Energetics
METABOLISM

1) The thermodynamic laws governing energy transformations and the concept of free energy.
2) The role of enzymes that regulate chemical reactions that control metabolism.
3) The structure and function of enzymes, along with the factors that affect their activity.
4) The role of REDOX reactions in electron-carrier molecules in cell respiration.
5) The metabolic steps of cellular respiration and fermentation pathways to generate energy.
6) The role of pigments in electron capture and the metabolic steps of photosynthesis.
7) The factors affecting the rate of cell respiration, fermentation & photosynthesis.
Name: _____________________ Teacher: ______________
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2.1 THERMODYNAMICS & FREE ENERGY
Metabolism = sum of all the chemical reactions in a cell
● Controlled by ENZYMES.
● Cell reactions are coordinated with each other and occur in sequences called metabolic
pathways, with each step catalyzed by a specific enzyme, encoded by a specific gene:
● Involve coupling of ANABOLIC & CATABOLIC pathways:
__________________ pathways
= release energy by breaking down
complex molecules to simpler ones.
_____________________ pathways
= consume energy to build complicated
molecules from simpler ones.
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ENERGY: SOME BASIC PRINCIPLES
Energy = ability to do WORK!
Two types of energy exist and energy is constantly being converted between these two forms:
KINETIC ENERGY (Ek) POTENTIAL ENERGY (E p)

= energy of motion = energy of storage
Examples: Examples:
Thermodynamics = study of energy transformations
● Closed system - is isolated from its surroundings
● Open system - energy can transfer between system and surroundings
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ENTROPY (S) = measure of disorder
● every process ↑ entropy in the universe
● entropy of a system may ↓, but the entropy of the surrounding world ↑
Think about it – it’s true! An example to convince you…
Cars only convert about 25% of the potential energy in

the chemical bonds of the octane gas to move the car,
leaving 75% to be lost as heat and smoke.
The bottom line is…

We suck at energy transformation!
Organisms are < 100% efficient energy transducers!

Organisms consume well-ordered food products as fuel to build their own macromolecules, but
then release disordered indigestible wastes and heat back into their surroundings.
Combining the 1st & 2nd laws of thermodynamics, we can conclude:

The quantity of energy in the universe is constant, but the quality is not.
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An ecology application of energy transformation…
Due to non-predatory death, excretion, and respiration, a significant amount of energy is lost to
the environment instead of being absorbed for production by consumers.
Energy transfer between trophic levels is generally inefficient, such that net production at one
trophic level is generally only 10% of the net production at the preceding trophic level…this is
known as the Ten Percent Law.
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Free Energy (∆G)
Free energy is the ability to do _______________ !
∆G = ∆H - T∆S
So, what does this equation mean?
1. Indicates the maximum amount of a system’s energy that is available to do work.

2. Indicates whether a reaction will occur spontaneously or not.
Spontaneous processes Nonspontaneous processes
occur without outside help occur if energy is added to the system
Spontaneous processes can…
● be harnessed to perform work

● increase the stability of a system
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Exergonic Reaction Endergonic Reaction
● digesting polymers ● building polymers
● hydrolysis = catabolism ● dehydration = anabolism
▪ energy released ▪ energy input

▪ spontaneous ▪ not spontaneous
▪ entropy increases ▪ entropy decreases
When equilibrium occurs, no heat energy is being lost or gained, and no

disorder is being lost or gained, since at equilibrium, it seems like reactions
aren’t occurring at all! This means ∆G = 0. Luckily, equilibrium only occurs in
closed systems – systems that do not interact with their surroundings.
Living organisms are definitely open systems, as they interact constantly with
their environments, so never reach equilibrium. If they did, their free energy
would be zero, meaning that they have absolutely no energy available to do any
sort of work – not so good at all. Any organism with ∆G = 0 is dead!
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Free Energy Practice Problems
1) Consider the coupled reactions below. State whether the reaction is endergonic or exergonic.
Burning firewood = ____________________
Heating water = ______________________
Glucose combustion = ___________________
ATP formation = ______________________
2) Complete the following table, showing all calculations. Convert units as needed!
Temp ΔH ΔS ΔG Ender or Exergonic?

Reaction (K) Enthalpy Entropy Free Energy
Spontaneous or not?
(kJ/mol) (J/K) (kJ/mol)
A A + B → AB 298 +12 -5
B CD → C + D 298 -32 +25
C CH4 + 2O2 → 298 -890 -243

CO2 + 2H2O
D N2 + 3H2→NH3 298 -92 -199
E 2COCl2 + H2O→ 284 -223 +284

CO2 + 2HCl
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2.2 enzymes
PROPERTIES OF ENZYMES
● Are protein catalysts (they speed up chemical reactions).

● Highly specific (a specific substrate binds to the enzyme’s active site).
● Reusable (enzymes are unaffected by the reaction).
● Many times have an “ase” ending.
● Some catalyze both forward and reverse chemical reactions.
● INDUCED-FIT MODEL: Enzyme-substrate interaction is more than just lock and key.
● Typically substrates are

held in the active site by
weak intermolecular
interactions, such as
H-bonds and ionic bonds.
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Enzymes “Lower” Activation Energy
● Activation energy is the amount of energy necessary to push the reactants over an energy
barrier in a chemical reaction (even exergonic reactions require an activation energy).
● Enzymes speed up reactions by lowering energy barriers (EA).
● Note: Enzymes do not lower delta G.
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FACTORS THAT AFFECT ENZYME ACTIVITY
ENZYME CONCENTRATION
● As ↑ enzyme, ↑ reaction rate.

● More enzymes = more frequently collide with the substrate.
SUBSTRATE CONCENTRATION
● As ↑ substrate = ↑ reaction rate. More substrate = more frequent collision with enzyme.
● Reaction rate levels off (“enzyme saturation”). All enzymes have active sites engaged.
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TEMPERATURE
● Specific enzymes work best at a specific optimum temperature.

● Human enzymes optima 35°- 40°C.
Heat: Cold:
Increase activity beyond optimum T°. Decrease activity in cold T°.
Increased energy level of molecules disrupts Molecules move slower, decreasing collisions
bonds leading to denaturation (=lose 3D shape). between enzyme and substrate.
pH
Changes from the optimal pH: adds or remove H+,

disrupting bonds holding together the 3D shape of
the protein (=denaturation).
SALINITY
If salt concentration is too high,

normal interactions of charged groups
will be blocked, forming a precipitate.
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ACTIVATORS
Many enzymes require non-protein cofactors for catalytic activity.
Inorganic Cofactors: include Zn, Fe, and Cu.

Organic Cofactors: coenzymes, include vitamins or molecules derived from vitamins.
INHIBITORS
Molecules that reduce enzyme activity.
COMPETITIVE INHIBITION:
If inhibitor binds to the same site as the substrate, then it blocks substrate binding.
Example: Penicillin blocks enzyme bacteria use to build cell walls.
NON-COMPETITIVE INHIBITION:
Binding by the inhibitor at the allosteric site causes the active site to be closed off.
Example: Some anti-cancer drugs inhibit enzymes involved in DNA synthesis
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FEEDBACK INHIBITION
● Reversible inhibition of enzymes is a natural part of the regulation of metabolism.
● Molecules that naturally regulate enzyme activity often behave like reversible noncompetitive
inhibitors by binding weakly to an allosteric site to inhibit/stimulate enzyme activity.
● Common method of metabolic control is feedback inhibition.

● When the product is abundant the pathway is turned off.
● The inhibitor binds to the allosteric site which causes the active site to “close”.
● End product acts as an allosteric inhibitor of an enzyme found earlier in the pathway.
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2.3 ENERGY MOLECULES
In ecosystems, energy enters as sunlight and photosynthetic organisms

convert this light energy into chemical energy stored in the bonds of
organic molecules such as glucose. Glucose catabolism occurs through a
series of enzyme-catalyzed & coupled reactions, including REDOX
REACTIONS. Some of the energy released from the chemical bonds of
food is harvested and used to do work, while the rest is dissipated as heat.
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OXIDATION-REDUCTION REACTIONS (aka “REDOX”)
Involve electron transfer

between two substances, with LOSS of electrons is _________________
one substance being oxidized

and the other being reduced. GAIN of electrons is _________________
Oxidation Reduction
Electrons
Oxygen atoms
Hydrogen
Atoms
Memory Aid!
“O I L R I G”
&
“L E O the lion says G E R”
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Example 1: Formation of table salt is a redox reaction involving ionic bonds.
Sodium is oxidized and chlorine is reduced (its charge drops from 0 to -1).
The electron donor (Na) is the reducing agent and reduces Cl.
The electron recipient (Cl) is the oxidizing agent and oxidizes Na.
Example 2: The combustion of methane is a redox reaction involving covalent compounds.
Redox reactions also occur when the movement of electrons is not complete but
involve a change in the degree of electron sharing in covalent bonds.
In this reaction, the nonpolar covalent bonds of methane (C-H) and oxygen (O=O)
are converted to polar covalent bonds (C=O and O-H).
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The chemical equation for (aerobic) cell respiration demonstrating redox transfer:
Glucose and O2 are stable covalent compounds,

but when in contact, the oxygen atoms in the O2
molecules attract the electrons of the H-C bonds
in glucose. Thankfully, O2 is not a strong enough
oxidizer to strip electrons from these bonds just by
bumping into glucose at room temperature.
ACTIVATION ENERGY prevents spontaneous combustion,

which allows cells to control the oxidation process!
HOW DOES GLUCOSE COMBUSTION COMPARE IN…
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ENERGY CARRYING MOLECULE
ATP (adenosine triphosphate) is the key energy molecule in a cell due to the close packing
of three negatively-charged phosphate groups is an unstable, energy-storing arrangement.
Energy is released through the hydrolysis of ATP, which occurs quite easily as the P-O
bond is relatively unstable (due to repulsions between many negative charges on the O
atoms of the 3 crowded phosphate groups) and thus easy to break, yielding the more
stable combo of Pi (inorganic phosphate) and ADP.
ATP is an “energy coupler”, meaning that it has the ability of turning an endergonic and
non-spontaneous reaction into a one that is exergonic and spontaneous!
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It accomplishes this through…
PHOSPHORYLATION =
Now, this makes ATP a pretty awesome molecule!
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TWO WAYS TO MAKE ATP
Substrate-Level Direct formation of ATP via one enzyme catalyzed reaction, in which a
Phosphorylation phosphate-containing molecule transfers a phosphate group to ADP.
In aerobic cell respiration, only _____ ATP molecules (out of maximum 38

ATP) are made by substrate-level phosphorylation.
Oxidative
ATP is produced indirectly through a series of redox reactions, in which
Phosphorylation
electrons are passed from organic molecules, to electron carrier coenzyme
molecules such as NAD+ and FADH, and ultimately passed to O2.
In aerobic cell respiration, the majority of ATP (_____ ATP molecules out of
maximum 38 ATP) are made by oxidative phosphorylation.
This occurs in the “______________________” part of cell respiration.
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ENERGY (“ELECTRON”) CARRYING MOLECULES
● Energy can also be transported by other carrier molecules.

● Energy from exergonic reactions can be stored in electrons.
● These electrons are captured by electron carriers.
There are two types of energy

carrier molecules:
NADH & FADH2

NADH and FADH2 each carry
TWO electrons to the electron
transport chain so that ATP can
be made by oxidative
phosphorylation.
Compound Electrons Hydrogen

- oxidized or reduced? - lost or gained? – lost or gained?
NAD+
NADH
FAD
FADH2
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NAD+ gains H atoms from glucose and is reduced to NADH.
NADH This redox reaction is catalyzed by the enzyme NADH dehydrogenase.
NADH is derived from vitamin ______ (niacin) found in various meats, nuts and seeds.
FAD works like NAD+.

FADH2 It gains H atoms from glucose, undergoing a reduction to FADH2.
FADH2 is derived from vitamin (riboflavin)

________ found in organ meats (liver,
kidney, heart) and certain plants such as
almonds, whole grains, soybeans, green
leafy vegetables.
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2.4 AEROBIC CELL RESPIRATION
Cell Respiration General Equation:
C6H12O6 + 6O2 → 6CO2 + 6H2O + 36-38 ATP
“Aerobic” Respiration - cellular respiration in the presence of oxygen
FOUR STAGES OF AEROBIC CELL RESPIRATION
1. ___________________________ occurs in the _____________________.
2. ___________________________ occurs in the _____________________.
3. ___________________________ occurs in the _____________________.
4. ___________________________ occurs in the ____________________
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STAGE 1: GLYCOLYSIS
Defined as…
The reactions in which a glucose molecule (6C) is catabolized into 2 pyruvate molecules
(3C).
Occurs in…
Yields…
Overall Reaction:
NOTE!
Glycolysis occurs whether O2

is present or not.
If O2 is present, pyruvate moves

to the Krebs cycle and the energy
stored in NADH can be converted
to ATP by the electron transport
system and oxidative
phosphorylation.
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STAGE 2: PYRUVATE OXIDATION
Defined as…
The reactions in which pyruvate molecules (3C) are oxidized to form acetyl-CoA
molecules (2C), involving coenzyme A.
Occurs in…
Yields…
Overall Reaction:
Role of Coenzyme A in pyruvate oxidation…

Acts like a helper molecule when it attaches to acetyl (2C)
because it escorts the molecule to Krebs cycle.
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STAGE 3: KREBS CYCLE (aka “citric acid cyle”)
Defined as…
Catabolism of acetyl-CoA into CO 2 molecules and more electron carrying molecules.
Occurs in…
Yields…
Overall Reaction:
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STAGE 4: ELECTON TRANSPORT CHAIN
Defined as…
Transfer of electrons and protons from NADH and FADH2 in a series of increasing
electronegativity in compounds, eventually reaching O2, the most electronegative
compound, to form water. The free energy generated by the electron transport chain is
coupled to oxidative phosphorylation to generate ATP.
Occurs in…
Yields…
Overall Reaction:
ATP production prior to ETC:
Glycolysis = 2 ATP (net)

Krebs = 2 ATP
4 ATP
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Enter electron carriers NADH & FADH2…
They will each donate 2 electrons to the ETC (oxidation).
Description of the ETC…
A series of organic molecules, enzymes, protein complexes and O 2 organized

according to increasing electronegativity, with O2 being the most electronegative (final
electron acceptor).
The ETC is located in the inner membrane of the mitochondrion.
Movement of electrons through the ETC…
NADH is oxidated (loses 2 electrons) to the weakest attractor of electrons NADH

dehydrogenase, which now undergoes a reduction (gain of 2 electrons).
Electrons continue to transfer between ETC components via redox reactions until reaching
O2, the most electronegative molecule, in order to produce water.
At certain ETC components, protons are pumped into the intermembrane space of the
mitochondrion from the matrix in order to establish an electrochemical gradient.
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Production of the proton gradient…
At key compounds of the ETC, protons are pumped

out of the matrix into the intermembrane space to
establish a high concentration of protons.
This helps create the “proton motive force”.
Difference in starting points of NADH and FADH2 in the electron transport chain…
NADH = loses its electrons at NADH dehydrogenase, thus has the potential of pumping
out three protons (thus, 3 ATP can be made).
FADH2 = loses its electrons at Q, thus has the potential of pumping out two protons (thus,
2 ATP can be made).
Role of ATP synthase...
Protons re-enter the matrix via the ATP

synthase motor down its concentration
gradient in order to drive the production
of ATP by oxidative phosphorylation.
For every one proton, one ATP gets
made.
Chemiosmosis is defined as…
The movement of protons down its

concentration gradient back into the
matrix via the ATP synthase complex.
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NADH from cytoplasm produced during glycolysis enters into the
mitochondrion via two different shuttle systems…
Malate-Aspartate Shuttle
= NADH enters “as is”, thus 3 protons pumped out and that gives 3 ATP.
Glycerol-Phosphate Shuttle
= NADH converts to FADH2, thus 2 protons pumped out and that gives 2 ATP.
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Maximum 38 ATP yield occurs when…
NADH from glycolysis enters the matrix via the malate-aspartate shuttle.
Actual yield of ATP per one molecule of glucose is around 33 ATP, why?
Protons (H+) are “leaky”, meaning some are lost to other metabolic reactions.
Efficiency of cellular respiration in producing ATP (chemical energy)…
Per glucose molecule, 40% of energy is harvested for ATP while 60% is lost as
heat…again, we “suck” at energy transformation (back to the 2nd law of thermodynamics!).
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The rate of catabolism is regulated by FEEDBACK INHIBITION,
such that catabolism of glucose speeds up if ATP levels drop
and slows down if there is sufficient ATP.
Cell respiration is controlled by________________________
(the 3rd enzyme of glycolysis) that works

by ALLOSTERIC INHIBITION.
_______________________
= STIMULATOR of
phosphofructokinase
_______________________
= INHIBITOR of
phosphofructokinase
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2.5 ALTERNATIVE PATHWAYS
Glycolysis can accept a wide range of carbohydrates other than glucose.

Other sources of fuel other than carbohydrates include proteins and lipids.
These fuels “tap into” the cell respiration pathway to generate energy.
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PROTEIN CATABOLISM
● Proteins must first be digested to individual amino acids.
● Converting amino acids into energy is a two-step process:
STEP 1:
The amino group of the amino acid is removed in a process called DEAMINATION and is
converted to ammonia (NH3) which is then converted to urea and eliminated in urine.
STEP 2: The remaining intermediates either enter pyruvate oxidation or Krebs cycle.
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LIPID CATABOLISM
● Lipids must first be digested glycerol head and fatty acid tail components.
● Each subunit enters a different point in the energy-extracting pathway:
(1) The glycerol portion enters the glycolysis pathway.

(2) The fatty acid portion enters into Krebs cycle.
115
Outcome of glycolysis
when O2 is present…
Pyruvate enters into the

mitochondria and the remainder of
aerobic cell respiration follows for
full ATP production.
Outcome of glycolysis
when O2 is absent…
Pyruvate remains in the cytoplasm,

thus full ATP production using the
ETC cannot be achieved.
Under anaerobic conditions, various fermentation pathways generate ATP by glycolysis

and recycle NAD+ by transferring electrons from NADH to
pyruvate or derivatives of pyruvate.
MUST KEEP GLYCOLYSIS GOING, MUST KEEP GLYCOLYSIS GOING

116
TYPES OF FERMENTATION
ETHANOL FERMENTATION
In alcohol fermentation, pyruvate is

converted to ethanol in two steps,
one of which releases CO2 gas.
Examples:
● Bread making
● Alcolic drinks (wine, beer)
LACTIC ACID FERMENTATION
During lactic acid fermentation, pyruvate is

converted to lactate in a single step:
Examples:
● Anaerobic muscles
● Pickles
● Yogurt
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Facultative Anaerobes:
Are cells/organisms that perform either cell respiration

aerobically or anaerobically depending on whether O2 is
present such as muscle cells.
Obligate Anaerobes:
Are cells/organisms that can only perform anaerobic cell respiration (are poisoned by O2).
Examples include disease-causing pathogens such as…
TETANUS GANGRENE BOTULISM

caused by caused by caused by
Clostridium tetani Clostridium perfringes Clostridium botulinum
Called “lock jaw”, bacteria in Death of cells in extremities One of the most lethal
the body produces a due to lack of blood flow neurotoxins blocking nerve
neurotoxin that affects supplying oxygen, often function, leading to
muscles and nerves, lethal if associated with infection, respiratory and muscular
left untreated. diabetes, or resulting from paralysis.
frostbite.
118
2.6 PHOTOSYNTHESIS
Photosynthesis is… the conversion of light energy into chemical energy stored in
the bonds of sugar created.
Overall Equation:
CO2 + H2O C6H12O6 + O2
Photosynthesis is performed by organisms such as…
● Plants & some protists like algae, diatoms, dinoflagellates (have chloroplasts)
● Some bacteria like cyanobacteria (have pigments packaged in specialized membranes)
Photosynthesis in a Plant:
▪ Photosynthesis takes place within

organelles called CHLOROPLASTS.
▪ The main photosynthetic organs of

plants are LEAVES which are well
adapted for photosynthesis given
their large surface area for light
capturing.
▪ The photosynthetic tissue of a leaf is

called the MESOPHYLL.
▪ The green-coloured pigment that

carries out most photosynthesis is
CHLOROPHYLL.
▪ Chlorophyll pigments are clustered in

membranes called THYLAKOIDS.
▪ Regions where thylakoids are closely

stacked together are called GRANA.
▪ The fluid region surrounding thylakoid

membranes is called the STROMA.
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General Stages of Photosynthesis
Photosynthesis can be divided into two distinct stages:
LIGHT REACTIONS CALVIN CYCLE

“Light Dependent Reactions” “Light Independent Reactions”
• Occurs in thylakoids of chloroplasts. • Occurs in stroma of chloroplasts.

• Convert solar energy to chemical energy. • CO2 incorporated into organic molecules.
Energy Carrier Molecules in Photosynthesis:
▪ The initial energy that fuels photosynthesis comes from the SUN!
▪ This LIGHT energy is converted to CHEMICAL energy of two

different energy-carrying or storing molecules. This energy is
required to build carbohydrate molecules.
▪ The two energy-carrying molecules are that are produced in the light reactions and
help fuel the Calvin cycle:
1) NADPH
2) ATP
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Light Capture by Chloroplasts
▪ The sun radiates the full spectrum of electromagnetic energy.
▪ The narrow band from 380 to 750 nm (visible light) is biologically most important.
▪ When light hits a chloroplast, it is either

REFLECTED, TRANSMITTED or ABSORBED.
ABSORPTION SPECTRUM ACTION SPECTRUM
▪ Obtained from samples of pigment. ▪ The rate of photosynthesis is measured

at different wavelengths.
▪ Different wavelengths of light are passed
through and the absorption is measured. ▪ The maximum rate of photosynthesis
occurs at the blue and red ends of visible
▪ Blue and red light is absorbed, and
spectrum.
green light is reflected.
▪ Lowest rates are in the yellow-greens.
Relationship between the two graphs:

Blue and red light are the main peaks of light absorption and are responsible for the
peaks in the photosynthesis rate. The low absorption of green corresponds to its
reflection and the apparent green colour of chlorophyll and plants.
121
Pigments of Photosynthesis
▪ Photosynthetic pigments are located in clusters in the thylakoid membrane.
▪ In green plants, the main pigment is chlorophyll which has two main types:
o Chlorophyll a = _________________ in colour
o Chlorophyll b = _________________ in colour
▪ Other non-chlorophyll pigments called “accessory pigments” include:
o Carotenoids = _____________ coloured

o Phycoerythin = ____________ coloured
o Xanthophyll = _____________ coloured
o Lycopene = _______________ coloured
o Anthocyanin = _____________ coloured
o Phycocyanin = _____________ coloured
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Photoexcitation of Pigments:
▪ Pigments are excited by light (hence, “photoexcitation”):
If isolated chlorophyll pigments absorb In living photosynthetic cells, when

light energy, an electron is boosted from its pigments are photoexcited, electrons are
“ground state” to an “excited state” (orbital of lost to electron-carrying systems
higher energy). That electron will then drop (photosystems) which them moves the
down to its normal energy state, with electrons via redox reactions in the light
excess energy being given off as heat and reactions to ultimately generate ATP and
fluorescence. NADPH.
Photosystem = a collection of pigments and special proteins involved in photosynthesis
▪ There are 2 parts to a photosystem:
1) Reaction Centre = A protein complex that

includes 2 special chlorophyll a molecules
and a molecule called the primary electron
acceptor.
2) Antennae Pigments = A light harvesting

complex composed of chlorophyll pigments
and other accessory pigments.
▪ Chlorophyll pigments and other accessory

pigments serve as “antenna pigments” that
function in harvesting light and funneling
electrons towards the reaction center.
123
▪ The number and variety of pigment molecules enable a photosystem to harvest light over a
large surface area and larger portion of the spectrum.
▪ There are 2 photosystems present in plants:
o Photosystem I = Called ______ because its absorption spectrum peaks at ______ nm.
o Photosystem II = Called ______ because its absorption spectrum peaks at _____ nm.
Light-Dependent Reactions: key components

Component Role
Water When water splits it produces:
1) Oxygen: to be used for cell respiration
2) Electrons: to replenish those lost by chlorophyll photoexcitation
3) Protons: to contribute to proton pool in thylakoid lumen
Z Protein
Enzyme associated with photosystem II that helps split water.
B6-f Complex
ETC component that brings protons from stroma into the thylakoid lumen.
NADP
ECT component that catalyzes the reduction of NADP+ to produce NADPH.
reductase
ATP
Chemiosmotic gradient that produces the proton motive force that motors the
synthase
ATP synthase complex to produces ATP released into the stroma.
124
125
▪ There are 2 possible routes for electron flow in the light reactions:
Non-Cyclic Flow Cyclic Flow

Called non-cyclic because electrons Called cyclic because electrons that
do not return to reaction centre leave PSI eventually return there.
(rather, electrons carried by NADPH).
Predominance
Stimulated under certain
Is the predominate route.
conditions.
Photosystems
Involved Involves both PSI & PSII. Involves PSI only.
Generates
Generates ATP, NAPDH and O 2 Generates extra ATP
(no NADPH or O2).
126
Calvin Cycle Reactions: three stages
Stage Description of Stage
Carbon Incorporation of atmospheric CO2 into RuBP using the enzyme

Fixation RUBISCO to make PGA.
Reduction Conversion of PGA (3-carbon sugar) into G3P (another 3-carbon sugar)
Reactions using ATP and NADPH.
RUBP Regeneration of G3P (3-carbon sugar) back into RuBP (5-carbon

Regeneration sugar), using ATP to create the double phosphorylation condition of
RuBP.
127
How does a plant deal with the problem of living in dry environment?
On hot, dry days plants close the stomata to conserve water.
What conflict does this present to a plant?
Closing stomata prevents gas exchange (CO2 in and O2 out) that

impacts the rate of photosynthesis, but also for the evaporative
loss of water that allows the plant to cool.
The “Standard” C3 Pathway

of Photosynthesis
In most plants (C3 plants), initial fixation of CO2

occurs via rubisco and results in a 3-carbon
compound, 3-phosphoglycerate (3PG).
When their stomata are closed on a hot, dry

day, CO2 levels drop as CO2 is consumed in the
Calvin cycle.
At the same time, O2 levels rise as the light

reaction converts light to chemical energy.
So, what’s the problem with RUBISCO?
While rubisco normally accepts CO2, when the

O2/CO2 ratio increases (on a hot, dry day with closed
stomata), rubisco can add O2 to RuBP…this is BAD
because it decreases photosynthesis output.
128
So, what happens if there is a higher O2 to CO2 ratio?
Photorespiration
When rubisco adds O2 to RuBP, RuBP
splits into a “good” 3-carbon molecule
(PGA) and a “bad” 2-carbon molecule
(phosphoglycolate).
So, why is phosphoglycolate “bad”?
Phosphoglycolate must be exported from the chloroplast and degraded to CO2 by

mitochondria and peroxisomes…this takes up valuable energy from the plant!
Photorespiration DECREASES photosynthetic output.

It can drain away as much as 50% of the carbon
fixed by the Calvin cycle on a hot, dry day.
FEAR NOT!
Nature has a way of solving problems.
129
Other pathways of photosynthesis than the “standard” C3 pathway
evolved to combat photorespiration in hot, arid climates…
Both pathways involve “fixing” CO2 in the form of an intermediate molecule called OAA
(oxaloacetate) using the enzyme PEPase. By doing so, OAA can either move or hold that
CO2 until it can stockpile it and release it, thereby acting as a CO2-concentrating mechanism.
This offsets the O2/CO2 ratio in its favour and minimizes the effect of photorespiration.
C4 PHOTOSYNTHESIS
In C4 plants, carbon fixation

and the Calvin cycle are
spatially separated.
Include corn, sugarcane and

many grasses found in
hot, dry climates.
PEPase “fixes” CO2 to OAA

and ships it to the bundle
sheath where acts to
concentrate the CO2 and the
rest of the Calvin cycle can be
completed.
C4 plants have characteristic

“Krantz Anatomy” with enlarged
bundle sheath cells having
numerous chloroplasts (C3
plants don’t have chloroplasts
in their bundle sheath cells).
130
CAM PHOTOSYNTHESIS
In CAM plants, carbon fixation and Calvin cycle are temporally separated.
Include cacti, succulents and pineapple found in hot, drought-prone climates.
Stomata remain closed during the day and only open at night to bring CO2 in.
PEPase “fixes” CO2 to OAA at night and during the day releases it to raise the
CO2/O2 ratio to offset photorespiration. OAA is stored in the vacuole, which forces
more water into the vacuole, hence CAM plants are “succulent”.
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132
Free Square Dots Graph Paper from http://incompetech.com/graphpaper/squaredots/
SBI4UAP | Unit 5
Hardy-Weinberg Equilibrium &
Chi-Square Statistics & Speciation
EVOLUTION

1) How microevolution allows populations to evolve due to gene frequency changes over time.
2) The application of Hardy-Weinberg equation to study changes in gene/allele frequencies.
3) The conditions needed in a population in order to maintain Hardy-Weinberg equilibrium.
4) The factors tied to microevolution (changes in allele frequencies in a population).
5) How Hardy-Weinberg equilibrium is modelled and the effects of selection.
6) The application of Chi-Square testing in biology problems.
7) The species concept, reproductive barriers & the process of speciation (allopatric vs. sympatric).
Name: _____________________ Teacher: ______________
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Unit 5 - Evolution Outline
TOPIC 5.1 | HARDY-WEINBERG EQUILIBRIUM Homework & Assessments
Lesson ● Hardy-Weinberg Equations 🖉 Hardy-Weinberg Practice Problems
1 ● Hardy-Weinberg Equilibrium
TOPIC 5.2 | MICROEVOLUTION Homework & Assessments

Lesson ● Causes of Macroevolution
2 ● Genetic Drift ***FOR QUIZ: Hardy-Weinberg Problem Solving
Activity – Simulating Genetic Drift

Lesson ● Hardy-Weinberg Case Studies 🖉 Evolution Cases Follow Up Questions
3 ● Heterozygote Advantage
Activity – Simulating Evolution
TOPIC 5.3 | CHI SQUARE STATISTICS Homework & Assessments

Lesson ● Chi-Square Hypothesis Testing 🖉 Chi-Square Practice Problems
4
Activity – M&M Statistics
Lesson ● Chi-Square & Genetics 🖉 Chi-Square Practice Problems
5
***FOR QUIZ: Chi-Square Problem Solving
TOPIC 5.4 | SPECIATION Homework & Assessments

Lesson ● Species Definition 🖉 Reproductive Barriers Practice Problems
6 ● Reproductive Barriers
● Mode of Speciation
● Tempo of Speciation
Lesson
7 “OF” Test – Population Genetics, Chi-Square Statistics & Speciation (end-unit test)
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5.1 HARDY-WEINBERG EQUILIBRIUM
A turning point for evolutionary theory was the birth of population genetics, a field interested in
determining how the genetic composition of populations changes from one generation to the next.
A comprehensive theory of evolution called “modern synthesis”, took form in the early 1940’s,
integrating varied ideas from paleontology, taxonomy, biogeography and population genetics.
The modern synthesis emphasizes:
1) __________________________ as the unit of evolution.
2) ______________________________ as the mechanism of evolution.
3) ________________ as the heritable units of evolution.
Hardy-Weinberg Principle
In early 1900s, Reginald Punnett wondered such things

as whether allele frequencies remain constant
generation after generation, or if changes such as
dominant alleles gradually becoming more abundant
and eventually fixed would occur. He asked Godfrey
Hardy, a mathematician, for his perspective and
immediately Hardy came up with a solution. Almost
simultaneously, Wilhelm Weinberg, a physician,
developed the same solution.
How Does it Work?
Most traits are depicted by (at least) 2 alleles, often where one is dominant and the other
recessive.
If p = the frequency of allele A, and q = the frequency of allele a, then:
ALLELE FREQUENCY FORMULA:

p=
q=
135
Assume that in any generation, each type of sperm had an equal chance to fertilize each type of
egg. Assign the letter p to the A allele and the letter q to the a allele; then,
Ova A a
Occurs with probability p Occurs with probability q
Sperm
A
Occurs with
probability p
a
Occurs with
probability q
GENOTYPE FREQUENCY FORMULA:

p2 =
2pq =
q2 =
The above equation, which describes a single locus with two alleles (e.g., A and a),
has been termed the…
136
Hardy-Weinberg Sample Problems
Example 1: Suppose the A allele as a frequency of 0.7, what are the genotype frequencies?
Example 2: About 1 in 10,000 babies born in the U.S. is born with PKU (phenylketonuria), which
results in mental disability if left untreated. The disease is caused by a recessive allele. What
percentage of people in the U.S. carries the PKU allele?
Example 3: Suppose you determine 16% of the human population has a continuous hairline (a
homozygous recessive trait), determine how many individuals are homozygous dominant and how
many are heterozygotes.
137
Example 4: Albinism is recessive to normal pigmentation in humans. The frequency of the albino
allele was 10% in a population. Determine the proportion of people that you would expect to be
non-albino.
Example 5: A population of cats contained 405,000 that were black in colour and 95,000 that were
white. The black phenotype is dominant to the white phenotype.
a) What are the allele and genotype frequencies?
b) If the black phenotype became fatal at birth, what would happen to p and q values over time?
c) If the white phenotype became fatal at birth, what would happen to p and q values over time?
138
Hardy-Weinberg theorem describes the
gene pool of a non-evolving population.
This theorem states that the frequencies of alleles and genotypes

in a population’s gene pool will remain constant over generations
unless acted upon by agents.
If allele frequencies change in a new generation compared to the

previous generation, then the population is not in Hardy-Weinberg
Equilibrium and this provides evidence for evolution!
Evidence of Evolution
The Hardy-Weinberg principle is used to show that allele frequencies remain constant from
generation to generation (i.e., no changes in the gene pool). When there have been no changes to
the genetic equilibrium (allele frequencies do not change from generation to generation) will only
occur when the following conditions have been met:
(1)
(2)
(3)
(4)
(5)
Shifting the Balance >> EVOLUTION!
However, in natural populations, all these conditions

are almost never met. Thus, significant deviations from
the expected Hardy-Weinberg values provide evidence
that some agent of evolution is in action (at least one of
the above conditions is not being met).
139
HARDY-WEINBERG PRINCIPLE
PRACTICE PROBLEMS
#1—This is a classic data set on wing coloration in the scarlet tiger moth (Panaxia dominula).
Coloration in this species had been previously shown to behave as a single-locus, two-allele system
with incomplete dominance. Data for 1612 individuals are given below. Calculate the allele and
genotypic frequencies.
White-spotted (AA) =1469 Intermediate (Aa) = 138 Little spotting (aa) =5
#2—9% of an African population is born with a severe form of sickle-cell anemia (ss).
A) What percentage of the population will be more resistant to malaria because they are heterozygous
(Ss) for the sickle-cell gene?
B) If the population has 9,000 people, how many are carriers of the sickle-cell gene?
#3—After graduation, you and 19 friends build a raft, sail to a deserted island, and start a new
population, totally isolated from the world. Two of your friends carry (that is, are heterozygous for) the
recessive cystic fibrosis (c) allele, which in homozygotes causes cystic fibrosis. Assuming that the
frequency of this allele does not change as the population grows, what is the recessive cystic fibrosis
allelic frequency on your island?
#4—In Drosophila (fruit fly), the allele for normal wing length is dominant over the allele for short wings.
In a population of 1000 individuals, 360 show the recessive phenotype. How many individuals would
you expect to be homozygous dominant for the trait.
#5—The allele for a widow's peak (hairline) is dominant over the allele for a straight hairline. In a
population of 500 individuals, 25% show the recessive phenotype. How many individuals would you
expect to be homozygous dominant and heterozygous for the trait?
#6—The allele for a hitchhiker's thumb is dominant over a straight thumb. In a population of 1000
individuals, 510 show the dominant phenotype. How many individuals are expected for each of the 3
possible genotypes for this trait?
#7—From the AP Biology exam from 1992: Two pirates and three Polynesian beauties (females) settle
on a previously uninhabited tropical island. All five settlers have brown eyes but one man carries a
blue eye gene (he is Bb).
A) When the population reaches 20,000 individuals, how many blue eyed people will be in the
population?
B) How many will be homozygous dominant for this trait and how many will be heterozygous?
#8—In an island cat population of 150 cats, 15 are albinos.
A) How many cats carry but do not show the albino gene?
A) If the cats increased to 750,000, how many of them will be homozygous dominant individuals?
How many will be albino?
B) What would you conclude if the number of albinos in reality turns out to be twice the number you
calculated in your answer to b?
140
141
142
143
144
Simulating Hardy-Weinberg Equilibrium
Case 1 - Test of an Ideal Hardy-Weinberg Population
General Procedure: The class will simulate a population of
randomly mating individuals, with a genotype distribution noted at
right. Upon finding a mate, the two cards representing alleles
carried by each individual will be randomly shuffled and each parent
will donate one allele to produce their offspring. Parents must
produce two offspring at the time of mating. The first offspring will
go to one parent, and the second offspring will go to the second
parent. Parents now assume the genotype of the offspring in the
subsequent generation.
CASE 1: H-W EQUILIBRIUM CLASS DATA

GREEN RED Gen #AA #Aa #aa
PERSON PERSON
Initial Genotype P
all
F1 Genotype F1
genotypes
survive F2 Genotype F2
F3 Genotype F3
F4 Genotype F4
F5 Genotype F5
Determine the final genotype and allele frequencies:
# of A alleles in the F5 generation: # of a alleles in the F5 generation:
# with genotype AA ____ X 2= ____ A alleles # with genotype aa ____ X 2= ____ a alleles
# with genotype Aa ____ X 1= ____ A alleles # with genotype Aa ____ X 1= ____ a alleles
Total = ____ A alleles Total = ____ a alleles
Frequency of A Allele in the F5 generation: Frequency of a Allele in the F5 generation:
p = Total # A alleles / Total # of alleles in population q = Total # a alleles / Total # of alleles in population
p= q=
Discuss how the final allele frequencies of the population changed from the parental population.
145
Case 2 – Effect of Selection on Hardy-Weinberg Equilibrium
General Procedure: For this case, you will follow the

procedure outlined in Case 1, only that homozygous recessive
(aa) genotypes never survive. For example, these individuals
have sickle cell anemia and don’t survive.
CASE 2: SELECTION CLASS DATA

PERSON PERSON
Initial Genotype P
aa genotype
F1 Genotype F1
always dies
F2 Genotype F2
Create another
F3 Genotype F3
child if you produce
a homozygous F4 Genotype F4
recessive child.
F5 Genotype F5
Determine the parental and final genotype and allele frequencies:
p= q=
146
SICKLE CELL DISEASE & MALARIA
In tropical Africa, where malaria is common:
Homozygous dominant (normal) HbHb

= die or reduced reproduction from malaria
Homozygous recessive (disease) HsHs

= die or reduced reproduction from sickle cell anemia
Heterozygote carriers (symptomatic) HbHs

= survive & reproduce more, more common in population
Malaria Life Cycle:

Single-celled eukaryote parasite
(Plasmodium) spends part of its life cycle in
red blood cells. It infects its hosts via a
mosquito vector.
Hypothesis:
In malaria-infected cells, the O2 level is
lowered enough to cause sickling which kills
the cell & destroys the parasite.
147
Case 3 – Heterozygote Advantage
General Procedure: For this case, you will follow the procedure
outlined in Case 1, only that homozygous recessive (aa) genotypes
never survive and the heterozygote genotype (AA) survives 50% of
the time – you need to flip a coin. This would parallel the situation
seen with individuals heterozygous for sickle cell who are more
resistant to malaria than homozygous individuals.
CASE 3: HETEROZYGOTE ADVANTAGE CLASS DATA

PERSON PERSON
Initial Genotype P
aa genotype
F1 Genotype F1
always dies
F2 Genotype F2
AA F3 Genotype F3
genotype F4 Genotype F4
dies 50% of
F5 Genotype F5
the time
F6 Genotype F6
F7 Genotype F7
Heads = AA dies
F8 Genotype F8
Tails = AA lives
F9 Genotype F9
F10 Genotype F10
Determine the parental and final genotype and allele frequencies:
p= q=
148
FOLLOW UP QUESTIONS
1. Explain how a deleterious allele can survive in a population when infected people die in childhood.
2. This activity reflected evolution occurring in a population of organisms. Can evolution realistically be
observed in such a short time period – for which organisms? Explain.
3. A striking example of heterozygote advantage mediated by inferiority of both homozygotes is found

among common rats (Rattus norvegicus) in Wales, UK. The poison warfarin is an anticoagulant
(prevents clotting of blood) has been used for a number of years to control rat population sizes.
A single genetic locus controls resistance to warfarin, and there is a stable

polymorphism in Welsh rat populations for a dominant resistance allele (R).
Homozygotes for the wild-type allele (S) are killed by warfarin, and homozygotes
for the resistance allele are disfavoured because they are highly susceptible to
vitamin K deficiency. As such, heterozygotes are at an advantage.
a) Speculate the mechanism by which the resistance allele (R) emerged in the
population and initially spread.
b) Suppose warfarin has been used for 10 years as a commercial pesticide, followed by a period of
strict non-use for five years. Predict the success of this pesticide in reducing rat population sizes
in the initial 10 year period and in the 5 year period that follows in the absence of pesticide.
Justify your answer.
149
5.2 microevolution
MICROEVOLUTION: Changes in a population’s allele frequencies generation to generation.
Allele frequency changes give evidence that

some agent of evolution is acting on the population.
Example 1:
Example 2:
150
There are FOUR factors contributing to microevolution.
#1 GENETIC DRIFT: Change in allele frequency within a

population that occurs purely as a result of chance.
Simulating Genetic Drift with Cards
A allele #A #a A allele #A #a
Generation Generation
Frequency alleles alleles Frequency alleles alleles
Parent 0.5 1 to 5 6 to 10 Parent 0.5 1 to 5 6 to 10
1 11
2 12
3 13
4 14
5 15
6 16
7 17
8 18
9 19
10 20
Genetic drift always

influences allele frequencies
to some degree, no matter
how large the population, but
affects small populations
more significantly.
Generally, genetic drift will

cause populations to lose
their heterozygotes, and to
become entirely comprised of
homozygous individuals.
151
Events Leading to Significant Genetic Drift
BOTTLENECK EFFECT
Genetic drift caused by a dramatic, often temporary, reduction in
population size (eg. disease, natural disasters, overhunting, etc.).
Small numbers of individuals left in the

population after the bottleneck increases
likelihood that genetic drift will influence
the composition of the population. When
alleles are lost, the population becomes
more susceptible to other negative effects
such as disease.
152
Example: Cheetahs have less than 1% diversity
(as if all cheetahs are identical twins!) due to two
bottlenecks that happened in the past (the first was
10,000 year ago during an ice age and the second
100 years ago due to poaching and habitat loss).
Explain the “EXTINCTION VORTEX” below which is an example of positive feedback.
153
FOUNDER EFFECT
Genetic drift that results when a small number of individuals
separate from their original population and found a new population.
Example: Amish communities originated by a small number of founding members who escaped
religious persecution in Europe in the 1800s. They had a higher frequency of polydactyly
(six-fingered) and shorter limbs compared to the general population. The founder effect is still
observed generations later due to limited mating outside communities.
154
#2 NATURAL SELECTION: Differential survival and
reproduction associated with a trait.
Natural selection will lead some

individuals to leave more offspring
than others potentially resulting in
changes in allele distributions.
Natural selection accumulates and

maintains favourable genotypes in a
population.
#3 GENE FLOW: Genetic exchange due to migration of

fertile individuals between populations.
Gene flow tends to reduce

differences between populations.
#4 MUTATION: Change in the organism’s DNA,

leading to variation of alleles.
New alleles originate only by mutation. Sexual reproduction produces unique

recombinations of the existing alleles in individuals from the population gene pool.
An individual mutant allele may have greater impacts later through increases in its relative
frequencies as a result of natural selection or genetic drift.
155
5.3 chi square statistics
Why do you always seem to get a package with
mostly brown M&Ms and not your favourite
colour? Does the Mars Company ensure that
each package gets a certain number of each
M&M colour? The information below comes from
the Mars Company website.
13% brown, 14% yellow,

13% red, 24% blue,
20% orange, 16% green
One way we can determine if the Mars Company is true to its claims is to sample a package of
M&Ms and complete a statistical test known as a chi-square test.
The formula for calculating chi-square (χ2) is:
State the NULL HYPOTHESIS:
156
PROCEDURE:
1. Separate the M&Ms into colour categories and count the number of each color.
2. Calculate the expected number of M&Ms in your package by multiplying the total
number of M&Ms in the package by the colour percent listed above.
For example, if your package contains 500 M&Ms, then the expected number of red
M&Ms is 20% (500 x 0.20).
3. Determine the chi-square (χ 2) observed value by completing the table.
Yellow Red Orange Blue Green Brown TOTAL
Observed (O)
Expected (E)
Difference
(O-E)
Difference Squared
(O-E)2
(O-E)2 ÷E
Σ(O-E)2 ÷E
Sum of all the values that are shaded grey.
4. Determine the probability (p) that the difference between the observed and expected
values occurred simply by chance . First determine the degrees of freedom.
5. Scientists are willing to accept a hypothesis if the probability that the difference between the
observed and expected results is greater than 5% (0.05). Based on the degrees of freedom
calculated above, determine the X2critical value that you will use to compare your X2observed value.
157
6. Next compare your X2observed and X2critical values:
If X2observed is LESS than X2criticial, then the null hypothesis is ACCEPTED.

Means there is no statistical difference between the expected and observed counts.
If X2observed is GREATER than X2criticial, then the null hypothesis is REJECTED.

Means there is a statistical difference between the expected and observed counts.
From these results, do you accept or reject your null hypothesis: __________________
This means that if the probability determined is greater than 5% (0.05) then
any differences between the observed colour counts and the claims of the
Mars Company is due to chance alone. Five percent! That’s not much … but
it’s good enough for scientists! If, however, the probability determined is less
than 5% (0.05) then any differences between the observed colour counts
and the claims of the Mars Company is not due to chance.
158
Part A: Flipping Coins
Two coins were each flipped 200 times. The results
did not work out to be 50-50, leaving the question if
this is due to random chance?
For COIN A, 108 heads and 92 tails resulted.
For COIN B, 120 heads and 80 tails resulted.
1. How many degrees of freedom were there in the coin flip experiments? _______
What X2critical value is needed at a P value of 0.05? _______
2. Using the statistical evidence, determine which is the trick coin and explain your reasoning.
159
Part B: Male-Female Sex Ratios
Naked mole rats are a burrowing rodent native
to parts of East Africa. They have a complex
social structure in which only one female (the
queen) and one to three males reproduce, while
the rest of the members of the colony function
as workers. Mammal ecologists suspected that
they had an unusual male to female ratio. They
counted the numbers of each sex in one colony
and found there were 52 females and 34 males.
1. State the null hypothesis: _______________________________________________
2. Complete the table below:
Sex Observed Expected O-E (O-E)2 (O-E)2

(O) (E) E
Female
Male
TOTAL Σ(O-E)2/E = Χ2obs
3. Determine X2critical at p = 0.05
Degrees of freedom = ________ X2critical = _________
4. Make a conclusion.
160
Part C: Habitat Preference
You have been wandering about on a seashore and
you have noticed that a small snail (the flat periwinkle)
seems to live only on seaweeds of various kinds. You
decide to investigate whether the animals prefer certain
kinds of seaweed by counting numbers of animals on
different species. These numbers are recorded below in
the table.
2. Complete the table below:
Sex Observed Expected O-E (O-E)2 (O-E)2

(O) (E) E
Serrated Wrack 45
Bladder Wrack 38
Egg Wrack 10
Spiral Wrack 5
Other Algae 2
TOTAL Σ(O-E)2/E = Χ2obs
3. Determine X2critical at p = 0.05
Degrees of freedom = ________ X2critical = _________
161
Part D: Primate Aggression
A zookeeper hypothesizes that changing
the intensity of the light in the primate
exhibits will reduce the amount of
aggression between the baboons. In
exhibit A, with a lower light intensity, he
observes 36 incidences of aggression
over a one month period. In exhibit B,
with normal lights, he observes 42
incidences of aggression. Should he
support or reject his hypothesis?
2. Set up a chi square table below:
162
Part E: Fruit Fly Genetics
EXAMPLE 1: CROSS BETWEEN FEMALE WITH WILD EYES AND A MALE WITH SEPIA EYES
1. First start by answering the following questions and setting up your predictions:
a) Is the cross autosomal or sex-linked?
b) Is the mutation dominant or recessive?
163
2. Construct a Punnett square to predict results of the P (parental) cross and the F1 cross.
P CROSS:
F1 CROSS:
3. According to the Punnett square results,

what are the expected phenotypic ratios of
the F1 and F2 offspring?
4. Record the total # of flies produced in the F2 generation (observed). Combine males and female
numbers (for same phenotype) if cross doesn’t appear sex-linked. Calculate the # of individuals that
would be produced from this cross (expected). To do this, multiply the expected ratio (or percent) by
the total number of flies produced in the cross. Calculate X2observed for the F2 generation.
Phenotype Observed (O) Expected (E) (O-E)2/E
Σ(O-E)2/E = Χ2obs
5. Use the Chi-Square Distribution Table to determine the percent probability that the observed
variation is due to random chance alone. Use p = 0.05.
Degrees of freedom = _____________ X2critical = _________________
6. Based on the answer to the previous question, should you accept or reject your hypothesis
regarding the pattern of inheritance for this cross? Explain.
164
EXAMPLE 2: CROSS BETWEEN FEMALE WITH WILD EYES & VESTIGIAL WINGS AND A
MALE WITH SEPIA EYES AND WILD WINGS
1. First start by answering the following questions and setting up your predictions:
a. Is the cross autosomal or sex-linked?
b. Is the mutation dominant or recessive?
165
2. Construct a Punnett square to predict results of the P (parental) cross and the F1 cross.
P CROSS:
______________ X ______________
(female genotype) (male genotype)
F1 CROSS:
______________ X ______________
(female genotype) (male genotype)
3. According to the Punnett square results, what are the expected phenotypic ratios of the F1 and F2
offspring?
166
4. Record the total number of flies produced in the F2 generation (observed). Combine males and
female numbers (for same phenotype) if cross doesn’t appear sex-linked. Calculate the number of
individuals that would be produced from this cross (expected). To do this, multiply the expected ratio
(or percent) by the total number of flies produced in the cross. Calculate X2observed for the F2
generation.
Phenotype Observed (O) Expected (E) (O-E)2/E
Σ(O-E)2/E = Χ2obs
7. Use the Chi-Square Distribution Table to determine the percent probability that the observed
variation is due to random chance alone. Use p = 0.05.
Degrees of freedom = _____________ X2critical = _________________
8. Based on the answer to the previous question, should you accept or reject your hypothesis
regarding the pattern of inheritance for this cross? Explain.
167
Part F: Corn Genetics
A large ear of corn has a total of 433 grains, including 271 Purple & starchy, 73 Purple & sweet, 63
Yellow & starchy, and 26 Yellow & sweet. Your tentative hypothesis is that this ear of corn was
produced by a dihybrid cross (PpSs x PpSs) involving two pairs of heterozygous genes resulting in a
theoretical (expected) ratio of 9:3:3:1.
Test your hypothesis using chi square. Use the space below to show all your work!
168
Part F: Hardy-Weinberg Equilibrium & newts
In a certain population of newts, being poisonous (P)
is dominant over not being poisonous (p). You count
200 newts, and 8 are not poisonous.
1. Calculate the allele frequencies of the parent population.
2. Fifty newts are washed downstream after a big storm and colonize a new pond. Calculate the
expected frequency and number of each genotype to be?
3. You count the new population of newts and find 21 homozygous poisonous newts, 23
heterozygous poisonous newts, and 6 homozygous non-poisonous newts. Conduct a chi-square
analysis to test if the initial (expected) and final (observed) populations are in Hardy-Weinberg
equilibrium. Use p=0.05.
Genotype Observed Expected Expected O-E (O-E)2 (O-E)2 /E

(individuals) (frequency) (individuals) (individuals)
Poisonous
PP (p2)
Poisonous
Pp (2pq)
Not Poisonous
pp (q2)
50 1 50
State null hypothesis: ___________________________________________________________
X2observed = _______ At p = _____ and df = ______ , the X2critical = _______
Accept or Reject Null Hypothesis: _________________________________________________
169
Part G: Hardy-Weinberg Equilibrium & moths
Two populations of moths are being studied, one in the lowlands and the other in the highlands over a 6
year period. The SCA locus is being quantitatively assessed and this locus has two alleles, B and W.
The numbers of counted individuals of each genotype are given in the tables below for each population.
Lowland BB BW WW
Population
Initial 57 121 62
Final 61 119 60
Upland BB BW WW
Population
Initial 38 83 59
Final 90 87 3
a) Conduct a chi-square to test if the initial (expected) and final (observed) populations are in H-W
equilibrium at both locations. Use the numbers of alleles instead of frequencies! Use p=0.05.
LOWLAND Allele Observed Expected O-E (O-E)2 (O-E)2 /E

POPULATION
B
State null hypothesis: ___________________________________________________________

Accept or Reject Null Hypothesis: ___________________________________________________
UPLAND Allele Observed Expected O-E (O-E)2 (O-E)2 /E

POPULATION
B
State null hypothesis: ____________________________________________________________

Accept or Reject Null Hypothesis: ___________________________________________________
b) Based on the chi-square results, is there evidence for evolution in either of the populations?
170
5.4 SPECIATION
WHAT IS A SPECIES? (It’s not easy to define one!)
Biological Species Concept
A species is a population or group of populations

whose members have the potential to interbreed with
each other in nature to produce viable, fertile
offspring, but who cannot produce viable, fertile
offspring with members of other species.
Thus, species are based on interfertility, not physical similarity:
The eastern and western meadowlarks may look Humans have considerable diversity, but we all
extremely similar, but differences in song help prevent belong to the same species because of our capacity
interbreeding between the two species. to interbreed.
No single barrier may be

completely impenetrable to
genetic exchange, but many
species are genetically
sequestered by multiple
barriers.
171
Reproductive Barriers: Categorized as prezygotic or postzygotic, depending on whether
they function before or after the formation of zygotes:
PREZYGOTIC BARRIERS POSTZYGOTIC BARRIERS

Impede mating between species or hinder Prevent the hybrid zygote from developing into a
fertilization of ova if members of different species viable, fertile adult when a sperm from one
attempt to mate. species fertilizes ovum of another.
Habitat Isolation: Two organisms using different Reduced Hybrid Viability: Genetic
habitats even in the same geographic area are unlikely incompatibility between the two species may abort
to encounter to even attempt mating. the development of the hybrid at some embryonic
stage or produce frail offspring.
Example: Two Thamnophis species of garter snakes
occur in the same areas but because one lives mainly Example: Occasional hybrids between frogs in genus
in water and the other is primarily terrestrial, they rarely Rana form, but do not complete development and
encounter each other. those that do are frail.
Behavioral Isolation: Many species use elaborate Reduced Hybrid Fertility: Even if hybrid
behaviors unique to a species to attract mates. offspring are vigorous, the hybrids may be infertile
and the hybrid cannot backbreed with either parental
Example: In many species, elaborate courtship displays
species.
identify potential mates of the correct species (fireflies)
and synchronize gonadal maturation.
This infertility may be due to problems in meiosis
Temporal Isolation: Two species that breed during because of differences in chromosome number or
different times of day, different seasons, or different structure.
years cannot mix gametes. Example: While a mule, the hybrid product of mating
Example: While the geographic ranges of the western between a horse and donkey, is a robust organism, it
and the eastern spotted skunk overlap, they don’t cannot mate (except very rarely) with either horses or
interbreed because the former mates in late summer donkeys.
and the latter in late winter.
Mechanical Isolation: Closely related species Hybrid Breakdown: In some cases, first
may attempt to mate but fail because they are generation hybrids are viable and fertile. However,
anatomically incompatible and transfer of sperm is not when they mate with either parent species or with
possible. each other, the next generation are feeble or sterile.
Example: With many insects, copulatory organs of
Example: To illustrate this, we know that different
closely related species do not fit together, preventing
cotton species can produce fertile hybrids, but
sperm transfer.
breakdown occurs in the next generation when
Gametic Isolation: Gametes of two species do not offspring of hybrids die as seeds or grow into weak
form a zygote because of incompatibilities preventing and defective plants.
fusion or other mechanisms.
Example: Internal fertilization - Female reproductive
tract not conducive to the survival of sperm from other
species.
Example: External fertilization – Egg and sperm
recognition molecules must be compatible in animals,
and a similar molecular recognition mechanism enables
a flower to discriminate between pollen of same and
different species.
172
REPRODUCTIVE ISOLATING MECHANISMS
173
Reproductive Barriers Practice Problems
1) What are limitations to the species concept?
2) In the following examples, classify the reproductive mechanism as either prezygotic or postzygotic
and describe the mechanisms by which the isolation is achieved (e.g., temporal isolation, hybrid sterility, etc.).
a) Some different cotton species can produce fertile hybrids, but hybrid in the next generation die
in their seeds or grow into defective plants.
Prezygotic / postzygotic (circle answer) Mechanism of isolation: _____________________
b) Many plants have unique arrangements of floral parts that stops transfer of pollen between
plants.
c) Two orchid species living in the same rainforest flower on different days and don’t form hybrids.
d) Different salamander species live in the same regions and habitats, occasionally hybridizing.
The hybrids generally do not complete development, and those that do are weak and don’t
survive long.
e) Two different species of cricket are indistinguishable except for different song pitches.
174
Patterns of Speciation
MODES OF SPECIATION: Two general modes of speciation are distinguished by the
mechanism by which gene flow among populations is initially interrupted:
ALLOPATRIC SPECIATION SYMPATRIC SPECIATION

Ranges don’t overlap, thus no gene flow. Ranges overlap, permitting gene flow.
Allopatric Speciation…stages leading to it:

(i) Moving into new environments: Some individuals may colonize a new area for a variety
of different reasons (i.e., competition for food, mates, space) away from the parent population.
Gene flow is still possible between the parent and distant populations.
(ii) Geographical isolation: Physical or climatic barriers (i.e., mountain ranges, glaciers, land bridges,
or splintering of lakes). These barriers may cut off those parts of the population that are the
extremes of the species range, so gene flow is prevented or rare.
(iii) Differential selection pressures: The isolated populations may be subjected to different
selection pressures, favouring individuals with traits that suit each particular environment.
As allele frequencies change for certain genes, the population can take on the status of a
subspecies.
(iv) Reproductive isolation: The separated populations (isolated subspecies) may eventually
differ so much that they are incapable of reproducing even if the barrier is removed and
species placed in the same environment.
175
An ancestral fish species was split by the formation of the Harris's antelope squirrel (A. harrisi) inhabits the canyon's
Isthmus of Panama 3.5 mya. The porkfish (A. virginicus) south rim (left). Just a few miles away on the north rim
inhabits the Caribbean Sea while the Panamic porkfish (A. (right) lives the closely related white-tailed antelope squirrel
taeniatus) is found in the Pacific Ocean. (A. leucurus).
RING SPECIES provide examples of what seem to be various stages in the gradual divergence of
new species from common ancestors:
CASE STUDY: Ensatina salamander expanded south from Oregon to California.
The California pioneers split into one chain of interbreeding populations along the coastal mountains and another
along the inland Sierra Nevada mountains, and form a ring around California’s Central Valley. Salamanders of the
different populations contrast in colouration and exhibit more and more genetic differences the farther south the
comparison is made. At the northern end of the ring, the coastal and inland populations interbreed and produce
viable offspring - in this area they appear to be a single biological species. At the southern end of the ring, the
coastal and inland populations do not interbreed even when they overlap - in this area they appear to be two
separate species.
176
Sympatric Speciation…different mechanisms in plants vs. animals:
PLANTS = Sympatric speciation can result from accidents during cell

division and/or from hybrids between different species that result in extra sets
of chromosomes, a mutant condition known as polyploidy.
Polyploidy: 3 or more complete sets of chromosomes (3N or greater).
Example: Many agriculturally important crops are products of polyploidy such as…
oats, cotton, potatoes, tobacco, and wheat.
ANIMALS = Sympatric speciation may result from gene-based shifts in

habitat or mate preference.
Niche Isolation: Occupying microhabitats, thus Leads To…

preventing encounters with other organisms in
different microhabitats as often. REPRODUCTION ISOLATION
Groups remain genetically
Sexual Selection: Selecting mates with isolated for so long that they
particular traits such as colour preference. become unable to reproduce.
CASE STUDY: Sympatric speciation is one mechanism proposed for the explosive
adaptive radiation of almost 200 species of cichlid fishes in Lake Victoria, Africa.
Cichlid species exhibit various habitat preferences

and have become specialized for exploiting
different food resources.
Differences have been reinforced by non-random

mating in which females select males based on a
certain appearance (sexual selection). Individuals
of two closely related sympatric cichlid species will
not mate under normal light because females have
specific color preferences and males differ in
colour. However, under light conditions that
de-emphasize colour differences, females will mate
with males of the other species, resulting in viable,
fertile offspring.
177
TEMPO OF SPECIATION: Two models relate to the timing of speciation events:
Gradualism Punctuated Equilibrium
Model Species diversify gradually over long spans Species diversification does not
states… of time, more at a constant tempo occur at a constant tempo.
Explanation Species appear to undergo modifications Changes occur rapidly. There are little
of the during relatively short periods of their total changes during times when the environment is
model… existence and then remained essentially stable and significant changes when the
unchanged. environment changes.
Advocates Darwin Gould & Eldridge

of model… (and long-standing view) (recent interpretation)
Illustration
of the
model…
Evidence Fossil record shows many species appear New species will appear suddenly in rocks
for the as new forms rather suddenly (fossil strata) of a certain age such as those in
model… ▪ persist essentially unchanged, Burgess Shale.
▪ then disappear from the record
178
1 2.2 1 2.2
2 _
H
1.008
The Periodic Table of the Elements H He
1.008
4.002
hydrogen hydrogen
helium
3 1.0 4 1.6 5 2.0 6 2.6 7 3.0 8 3.4 9 4.0 10 _
3,5
Li Be Atomic Number 15
3,5
2.2 Electronegativity
Valence: the most common valence in bold B C N O F Ne
6.9418
lithium
9.012
beryllium
Average Atomic Mass
P
30.97
Colour Key
solid
liquid
10.81
boron
12.01
carbon
14.01
nitrogen
16.00
oxygen
19.00
fluorine
20.18
neon
11 0.9 12 1.3
( ) indicates isotope with
gas 13 1.6 14 1.9 15 2.2 16 2.6 17 3.1 18 _
longest half-life
phosphorus synthetic 3,5 2,4,6
Na Mg23.00 24.31
Al Si P
26.98 28.09 30.97
S Cl Ar
32.07 35.45 39.95
sodium magnesium aluminum silicon phosphorus sulphur chlorine argon
19 0.8 20 1.0 21 1.4 22 1.5 23 1.6 24 1.7 25 1.6 26 1.8 27 1.9 28 1.9 29 1.9 30 1.7 31 1.8 32 2.0 33 2.2 34 2.6 35 3.0 36 _
3,4 2,3,5 2,3,6 2,4 2,3 2,3 2,3 1,2 2 3 4 3,5 2,4,6
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
39.10 40.08 44.96 47.88 50.94 52.00 54.94 55.85 58.93 58.69 63.55 65.39 69.72 72.61 74.92 78.96 79.90 83.80
potassium calcium scandium titanium vanadium chromium manganese iron cobalt nickel copper zinc gallium germanium arsenic selenium bromine krypton
37 0.8 38 1.0 39 1.2 40 1.3 41 1.6 42 2.2 43 1.9 44 2.2 45 2.3 46 2.2 47 1.9 48 1.7 49 1.8 50 2.0 51 2.1 52 2.1 53 2.7 54 _
1 2 2,4 3,5
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
85.47 87.62 88.91 91.22 92.91 95.94 (97.91) 101.1 102.9 106.4 107.9 112.4 114.8 118.7 121.8 127.6 126.9 131.3
rubidium strontium yttrium zirconium niobium molybdenum technetium ruthenium rhodium palladium silver cadmium indium tin antimony tellurium iodine xenon
55 0.8 56 0.9 57 1.1 72 1.3 73 1.5 74 2.4 75 1.9 76 2.2 77 2.2 78 2.3 79 2.5 80 2.0 81 2.0 82 2.3 83 2.0 84 2.0 85 2.2 86 _
1,3 1,2 2,4
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
132.9 137.3 138.9 178.5 180.9 183.8 186.2 190.2 192.2 195.1 197.0 200.6 204.4 207.2 209.0 (209.0) (210.0) (222.0)
cesium barium lanthanum hafnium tantalum tungsten rhenium osmium iridium platinum gold mercury thallium lead bismuth polonium astatine radon
87 0.7 88 0.9 89 1.1 104 _ 105 _ 106 _ 107 _ 108 _ 109 _ 110 _ 111 _ 112 _ 114 116
Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Rg Uub Uuq Uuh

(223.0) (226.0) (227.0) (261) (262) (266) (264) (269) (268) (281) (272) (285) (289) (292)
francium radium actinium rutherfordium dubnium seaborgium bohrium hassium meitnerium darmstadtium roentgenium ununbium ununquadium ununhexium
58 1.1 59 1.1 60 1.1 61 1.1 62 1.2 63 1.2 64 1.2 65 1.2 66 1.2 67 1.2 68 1.2 69 1.3 70 1.1 71 1.3
Lanthanide
Series Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
140.1 140.9 144.2 (144.9) 150.4 152.0 157.3 158.9 162.5 164.9 167.3 168.9 173.0 175.0
cerium praseodymium neodymium promethium samarium europium gadolinium terbium dysprosium holmium erbium thulium ytterbium lutetium
90 1.3 91 1.5 92 1.4 93 1.4 94 1.3 95 2.1 96 1.3 97 1.3 98 1.3 99 1.3 100 1.3 101 1.3 102 1.3 103 _
Actinide
Series Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
232.0 231.0 238.0 (237.0) (244.1) (243.1) (247.1) (247.1) (251.1) (252.1) (257.1) (258.1) (259.1) (262.1)
thorium protactinium uranium neptunium plutonium americium curium berkelium californium einsteinium fermium mendelevium nobelium lawrencium
Amino Acid Structures

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Trinity College School

BOOK #1 NAME: ___________________

Learning Objectives: In this unit, you will learn…

Name: _____________________ Teacher: ______________

***FOR QUIZ: Functional Groups

***FOR QUIZ: Water & Acid-Base Chemistry

Atomic number = # of protons

Mass number = # protons + # neutrons

Naturally Occurring Isotopes of Carbon

Three Main Types of Radiation

Unstable nucleus emits an alpha particle

Unstable nucleus emits an electron (beta particle).

When an unstable nucleus emits high-energy

Gamma often accompanies alpha & beta emission.

The half-life is constant, but is different for each

Parent isotope undergoes decay, while the

Examples of Useful Radioisotopes in Biology

(give specific isotope) (time period) (alpha, beta, gamma?)

A Used in archeological dating.

B Used in thyroid therapy.

C Used in nuclear reactors.

D Used in geological dating.

E Used in brain scans.

F Used in cancer therapy.

Atoms with incomplete valence shells interact by either sharing or

Two types of INTRAMOLECULAR forces:

ELECTRONEGATIVITY = Attraction of an atom for the electrons of a covalent bond.

Where are Electrons Located?

The shape of a molecule is determined by the

For atoms with electrons in both s and p

VSEPR THEORY stands for “Valence Shell Electron Pair Repulsion”

While intermolecular bonds are weak, collectively they have strength.

Two types of INTERMOLECULAR forces:

Bond Forms Relative Example – sketch it!

Weak, but Two molecules of HCl

Weaker Two molecules of Cl2

Molecular Shape: Molecular Shape:

Molecular Shape: Molecular Shape:

Draw a molecule of water hydrogen-bonded to four other water molecules:

Biologically Important Properties of Water

Characteristic Property Explanation Effect Example

ADHESION Water molecules form Capillary Capillary action causes

Water absorbs HIGH H-bonding causes Temperature Keeps constant body

HIGH H-bonding causes Evaporative Sweating/panting to cool

OTHER IMPORTANT WATER PROPERTIES

COLOURLESS WITH HIGH TRANSMISSION OF LIGHT

3) Discuss the solubility of the following substances with water.

b) ethanol e) potassium chloride

c) carbon dioxide f) phospholipids

b) water traveling up the xylem in plants e) ice forms on pond in winter

c) transport of glucose in bloodstream f) dog pants on a hot summer day

“Autoionization of Water” Although pure water is virtually 100% molecular, a small

Completely ionize in solution. Partially ionize in solution.

Completely ionize in solution. Partially ionize in solution.

ACID = proton ___________

BASE = proton ___________

Example: Acetic acid solution, CH3COOH (aq)

BUFFER: Resist changes to pH even when H+ or OH- are added.

Example: Carbonic acid/bicarbonate buffer

HCOOH (aq) + CN-(aq) < === > HCOO-(aq) + HCN(aq)

3) For each of the following:

ii) NH3 (a weak base)

Name: _______ Teacher:

❏ glucose + fructose = _ (sugar found in ___)

❏ glucose + glucose = _ (sugar found in ____)

❏ glucose + galactose = _ (sugar found in ___)