Unit 1 Emergent Properties Learning Log SY16
Lesson 1- Chemistry, Water, Carbon
EK 2.a.3 Organisms must exchange matter with the environment to
grow, reproduce, and maintain organization
Topic Presentation: click here
Note: This is a-3 part topic
Textbook Resources:
Campbell’s Biology: chapters 2, 3, 4
OpenStax Biology: Chapter 2
Biozone Pages: Volume 1: p. 11-13
Supplementary Resources:
“Crash Course: Biology” Videos: That's Why Carbon is a Tramp: Biology
#1” “Water- Liquid Awesome: Biology #2”
Bozeman Science: “Matter”, “Water: A Polar Molecule”, “Acids Bases
and pH”
Learning Objectives
LO 2.6 The student is able to use
calculated surface area-to-volume ratios
to predict which cell(s) might eliminate
wastes or procure nutrients faster by
diffusion. [See SP 2.2]
LO 2.7 Students will be able to explain
how cell size and shape affect the overall
rate of nutrient intake and the rate of
waste elimination. [See SP 6.2]
LO 2.8 The student is able to justify the
selection of data regarding the types of
molecules that an animal, plant or
bacterium will take up as necessary
building blocks and excrete as waste
products. [See SP 4.1]
LO 2.9 The student is able to represent
graphically or model quantitatively the
exchange of molecules between an
organism and its environment, and the
subsequent use of these molecules to
build new molecules that facilitate
dynamic homeostasis, growth and
reproduction. [See SP 1.1, 1.4]
Part 1: Chemistry
Questions to answer:
1. How common are the elements that living systems are made
out of?
2. Explain the relationship between matter and energy.
3. Why do atoms bond?
4. What is the cause of molecular polarity?
5. How does the type of bonds present in a substance influence
the chemical and physical properties of that substance?
6. If the breaking of bonds requires an input of energy (which it
always does), how is it possible that some chemical reactions
(like the burning of gasoline, for instance) can release energy
into the environment?
7. How do the properties of a compound like H2O or NaCl illustrate
the concept of emergent properties?
8. Why are radioactive elements useful for the study of biological systems?
Things you should make sure you understand: Please ask about these in class
● The periodic location, atomic number, number of valence electrons, and biological utility of S,P,O,N,C,H, along
with Ca, K, Na, & Cl.
● How energy interacts with atoms.
● The differences between ionic and covalent bonds.
● How to identify if a substance is covalent (molecular) or ionic.
● Basic differences between covalent and ionic substances
● How to identify if a molecule is polar or non-polar.
● How to determine the intermolecular forces that will exist in a substance.
● The cause of radioactivity.
Part 2: Water
Questions to answer:
1. Why are living things mostly made of water?
2. Draw a water molecule and indicate its polarity.
3. Explain how the structure of water molecules account for each of the following properties:
a. Cohesion
b. Adhesion
c. High Specific Heat
d. Floating Ice
e. Good Solvent Properties
f. Dissociation of water molecules
4. Explain 1 way that each of the above properties are useful for living systems.
5. Explain the relationship between the dissociation of water and the pH of a particular aqueous solution.
Things you should make sure you understand: Please ask about these in class
● The absolute need for water in terrestrial living systems.
● How the properties of water demonstrate the concept of emergence.
● How to determine the pH of a solution if given the concentration of hydronium or hydroxide ions.
Part 3: Carbon
Questions to answer:
1. Why is carbon central to the structure of all biological molecules?
2. Explain the concept of an isomer. As the number of carbon atoms in a molecule increases, what happens to the
number of possible isomers of that molecule?
3. Why is it significant that all biological systems use L-amino acids and D-sugars?
4. Draw each of the following functional groups:
a. hydroxyl
b. carbonyl (ketone)
c. carbonyl (aldehyde)
d. carboxyl
e. amino
f. sulfhydryl
g. methyl
h. phosphate
5. Why are molecules that contain carboxyl groups acidic?
6. Why are molecules that contain amino groups basic?
7. How large a change to the structure of an organic molecule has to be made for that molecule to have a major
difference in its effect on a living system?
Things you should make sure you understand: Please ask about these in class
● Why carbon is such a versatile atom.
● The different types of isomers that can exist.
● The properties of all of the functional groups in question #4.
Lesson 2: organic macromolecules
EK 4.A.1: The subcomponents of biological molecules and their sequence
determine the properties of that molecule.
Topic Presentation: click here Note: This is a-2 part topic
Textbook Reading:
Campbells Biology Chapter 5
OpenStax Biology: Chapter 3
Biozone Pages: Volume 1: Part 1- pp. 10, 14, 22-30; Part 2- pp. 15 - 21
Supplementary Resources:
“Crash Course: Biology” Videos: Biological Molecules - You Are What You
Eat: Biology #3
Bozeman Science: “Biological Molecules”, “The Molecules of Life”
Learning Objectives
LO 4.1 The student is able to explain the
connection between the sequence and
the subcomponents of a biological
polymer and its properties. [See SP 7.1]
LO 4.2 The student is able to refine
representations and models to explain
how the subcomponents of a biological
polymer and their sequence determine
the properties of that polymer. [See SP
1.3]
LO 4.3 The student is able to use models
to predict and justify that changes in the
subcomponents of a biological polymer
affect the functionality of the molecule.
[See SP 6.1, 6.4]
Part 1: Background, Carbohydrates, & Lipids
Questions to answer:
1. How are macromolecule polymers assembled from monomers?
How are they broken down?
2. How can you tell a biological molecule is a carbohydrate?
3. Explain the relationship between monosaccharides, disaccharides, and polysaccharides.
4. Why are starch and glycogen useful as energy storage molecules, while cellulose is useful for structure and
support? Why isn’t cellulose easily broken down?
5. How do herbivores solve the problem of cellulose digestion?
6. How can you tell a biological molecule is a lipid?
7. Chemically, what is the difference between a saturated fat and an unsaturated fat? How does this difference
affect the properties of the molecules?
8. How are triglycerides, phospholipids, and steroids similar? How do they differ?
Things you should make sure you understand: Please ask about these in class
● The chemical differences between the carbohydrates and lipids described in this presentation.
● The roles played by carbohydrates and lipids in biological systems.
Part 2: Proteins & Nucleic Acids
Questions to answer:
1. Why are proteins the most complex biological molecules?
2. Draw the structure of a general amino acid. Label the carboxyl group, the amino group, and the variable (‘R’)
group.
3. Draw the formation of a peptide bond between two amino acids.
4. How does the structure of the ‘R’ group affect the properties of a particular amino acid?
5. Define each of the following levels of protein structure and explain the bonds that contribute to them:
a. Primary; Secondary; Tertiary; Quaternary
6. How can the structure of a protein be changed (“denatured”)?
7. Draw a nucleotide. Label the phosphate, sugar, and nitrogenous base.
8. Explain the three major structural differences between RNA and DNA.
Things you should make sure you understand: Please ask about these in class
● How the structure of proteins and nucleic acids allow for their biological functions.
● How both protein structure and nucleic acid structure illustrate the concept of emergent properties.
● Why directionality and sequence are crucial for the structure and function of proteins and nucleic acids.
● How nucleic acids and proteins function in storage and expression of biological information.
Lesson 3: MEMBRANES
EK 2.b.1 Cell membranes are selectively permeable due to their structure.
Topic Presentation:
click here
Textbook Reading:
Campbell’s Biology Chapter 7
OpenStax Biology: Chapter 4: Section 4.5 & 4.6; Chapter 5: Section 5.1
Biozone Pages:
Volume 1: pp. 42, 43-45 (relevant parts), 46 (relevant parts), 48-49 (relevant
parts), 59-63.
Supplementary Resources:
“Crash Course: Biology” Videos: In Da Club - Membranes & Transport:
Biology #5
Bozeman Science: “A Tour of the Cell”, “Cellular Organelles”
Learning Objectives
LO 2.10 The student is able to use
representations and models to pose
scientific questions about the properties
of cell membranes and selective
permeability based on molecular
structure. [See SP 1.4, 3.1]
LO 2.11 The student is able to construct
models that connect the movement of
molecules across membranes with
membrane structure and function. [See
SP 1.1, 7.1, 7.2]
Questions to answer:
1. How does the structure of the cytoskeleton contribute to its function?
2. Diagram an individual phosopholipid and a bilayer of phospholipids. Label the hydrophillic head, and
hydrophobic tails in both.
3. Explain the Fluid Mosaic model of the cell membrane and describe the functions of the proteins that are
embedded in the membrane.
4. Diagram the cell membrane. Label the following parts: lipid bilayer, integral proteins, peripheral proteins,
cholesterol, cytoskeleton, extracellular matrix, glycoproteins, and glycolipids. Explain the function of each part
of the cell membrane in contributing to the functioning of the cell.
5. If cells can not visually inspect other cells, how do the cells of our immune system know if a particular cell they
encounter is part of us or part of another organism?
Things you should make sure you understand: Please ask about these in class
● The structure and function of cillia and flagella.
● The structure and functions of the three major components of the cytoskeleton (microfilaments, microtubules,
and intermediate filaments).
● Why particular substances will or will not be able to pass through the phospholipid bi-layer of the cell
membrane.
● How membrane-protein structure can allow for portions of the protein to be embedded in the membrane AND
allow portions to extend in to and out of the cell.
● The structure and function of the cell wall.
● The structure and function of the extracellular matrix.
● The differences in structure and function among the types of intercellular junctions found in cells (tight
junctions, gap junctions, desmosomes, and plasmodesmata)
Lesson 4- Transport
EK 2.b.2 Growth and dynamic homeostasis are maintained by the constant
movement of molecules across membranes.
Topic Presentation: click here
Textbook Reading:
Campbell’s Biology Chapter 7- sections 7.3-7.4
OpenStax Biology: Chapter 5: Sections 5.2 - 5.4
Learning Objective
LO 2.12 The student is able to use
representations and models to analyze
situations or solve problems qualitatively
and quantitatively to investigate
whether dynamic homeostasis is
maintained by the active movement of
molecules across membranes. [See SP
1.4]
Biozone Pages: Volume 1: pp. 63-71.
Supplementary Resources:
“Crash Course: Biology” Videos: In Da Club - Membranes & Transport: Biology #5
Bozeman Science: “Cell Membranes”, “Transport Across Cell Membranes”
Questions to answer:
1. How does the second law of thermodynamics allow for diffusion of substances?
2. How is active transport possible, since it contradicts the tendencies of the second law of thermodynamics?
3. Diagram one complete cycle of the Sodium-Potassium pump. Is this active or passive transport?
4. Is it possible for a solution to be both hypertonic and hypotonic? Why or Why not?
5. How do large molecules get taken in to or removed from the cell?
Things you should make sure you understand: Please ask about these in class
● The similarities and differences between simple diffusion, facilitated diffusion, and active transport.
● Where cells get the energy to power active transport.
● The relationship between osmosis and tonicity.
● The adaptive strategies of animal, plant, and protist cells for dealing with the tonicity of their environments.
Lesson 5- Domains and Prokaryotic Cellular Organization
EK 2.B.3 Eukaryotic cells maintain internal membranes that partition the
cell into specialized regions.
Topic Presentation: click here
Textbook Reading:
Campbell’s Biology Chapter 27 Sections- 27.1-27.3, 27.6
OpenStax Biology: Chapter 4: Section 4.1 & 4.2
Learning Objectives
LO 2.13 The student is able to explain
how internal membranes and organelles
contribute to cell functions. [See SP 6.2]
LO 2.14 The student is able to use
representations and models to describe
differences in prokaryotic and eukaryotic
cells. [See SP 1.4]
Biozone Reading:
Volume 1: pp. 295-299 (relevant sections), 301
Supplementary Resources:
“Crash Course: Biology” Videos: Unicellular Life- Bacteria, Archea, & Protists: Biology #35
Bozeman Science: “The Three Domains of Life”, “Bacteria”, “Archea”, “Eukarya”
Questions to answer:
1. Explain why the prokaryote/eukaryote dividing line represents a fundamental division among organisms.
2. Explain why we can infer that the Universal Common Ancestor of all life on earth was:
a. Unicellular
b. Heterotrophic
c. Used DNA as its genetic material
3. Draw and label a typical prokaryotic cell. Briefly describe the function of each part.
4. In eukaryotic cells, chloroplasts are the site of photosynthesis, and mitochondria are the site of aerobic cellular
respiration. How are bacteria able to carry out photosynthesis and aerobic cellular respiration without these
organelles?
5. Why do bacteria evolve so much faster than multicellular eukaryotes?
6. Generally speaking, why do antibiotics only affect bacterial cells and not eukaryotic cells?
Things you should make sure you understand: Please ask about these in class
● The differences between transformation, transduction, and conjugation, as methods of horizontal transfer of
genetic information among bacteria.
● The following modes of nutrition and give examples of organisms that utilize each one:
a. chemoheterotrophic nutrition
b. photoautotrophic nutrition
c. chemoautotrophic nutrition
d. photoheterotrophic nutrition
● Why archaea are placed in their own domain of life, even though they have only been known to science since
the 1970’s.
Lesson 6- Eukaryote Overview and Endomembrane System
EK 2.B.3 Eukaryotic cells maintain internal membranes that partition the
cell into specialized regions.
Topic Presentation: click here
Textbook Reading:
Campbell’s Biology Chapter 6
OpenStax Biology: Chapter 4: Sections 4.3 & 4.4
Learning Objectives
LO 2.13 The student is able to explain
how internal membranes and organelles
contribute to cell functions. [See SP 6.2]
LO 2.14 The student is able to use
representations and models to describe
differences in prokaryotic and eukaryotic
cells. [See SP 1.4]
Biozone Pages: Volume 1: pp. 31-33, 36-41, 43-45 (relevant parts), 46
(relevant parts), 47, 48-49 (relevant parts), 50-57.
Supplementary Resources:
“Crash Course: Biology” Videos: Eukaryopolis-The City of Animal Cells: Biology #4 Plant Cells: Biology #6
Videos By Paul Anderson: “Compartmentalization”, “A Tour of the Cell”, “Cellular Organelles”
Questions to answer:
1. Why is the cell theory significant (don’t just state the tenets, explain what it means and why it is a theory)?
2. How does the ratio of a cell’s surface area to volume place upward and downward limits on cell size?
3. How do organelles allow for increased complexity in cells?
4. Draw and label a typical eukaryotic cell. Briefly state the structure and function of the following organelles:
a. Nucleus
b. Ribosomes (free and bound)
c. Endoplasmic reticulum (rough and smooth)
d. Golgi Apparatus
e. Vesicles
5. Explain how each of the organelles above functions in the endomembrane system.
Things you should make sure you understand: Please ask about these in class
● How advances in microscopy led to advances in cytology.
● The benefits and disadvantages of light microscopy and electron microscopy.
● How the information system of cells (DNA->RNA -> Protein) allows for cells to accomplish all physiological
processes
Lesson 7- Matter & Energy Processing
EK 4.A.2: The structure and function of subcellular components, and
their interactions, provide essential cellular processes.
Topic Presentation: click here
Textbook Reading:
Campbell’s Biology Chapter 6 Sections- 6.4-6.5
OpenStax Biology: Chapter 4: Section 4.3 & 4.4
Biozone Pages: Volume 1: 43-45 (relevant parts), 46 (relevant parts), 4849 (relevant parts)
Supplementary Resources:
“Crash Course: Biology” Videos: Eukaryopolis-The City of Animal Cells:
Biology #4 Plant Cells: Biology #6
Bozeman Science: “Compartmentalization”, “A Tour of the Cell”,
“Cellular Organelles”
Learning Objectives
LO 4.4 The student is able to make a
prediction about the interactions of
subcellular organelles. [See SP 6.4]
LO 4.5 The student is able to construct
explanations based on scientific
evidence as to how interactions of
subcellular structures provide essential
functions. [See SP 6.2]
LO 4.6 The student is able to use
representations and models to analyze
situations qualitatively to describe how
interactions of subcellular structures,
which possess specialized functions,
provide essential functions. [See SP 1.4]
Questions to answer:
1. Explain why cells can’t “make energy”?
2. How is the structure of a lysosome related to its function?
3. Explain one normal function of lysosomes in a multicellular organism and one abnormal function.
4. Explain the functions of vacuoles and explain how they differ between plant cells and animal cells.
5. Draw a mitochondria. Label the matrix, cristae, inner membrane, outer membrane and intermembrane space.
6. Draw a chloroplast. Label the stroma, thylakoids, grana, outer membrane, inner membrane, and where
chlorophyll can be found.
Things you should make sure you understand: Please ask about these in class
● Why cells require energy, and how they acquire it.
● The different roles of glucose and ATP in cellular systems.
● Why mitochondria and chloroplasts are separate from the endomembrane system, and are considered “semiautonomous” organelles.
● The relationship between the processes that occur in the mitochondria and the processes that occur in the
chloroplast.
Lesson 8: Adult v. Fetal Hemoglobin
Enduring Understanding 4.C: Naturally occurring diversity among and
between components within biological systems affects interactions with
the environment.
Essential Knowledge 4.C.1: Variation in molecular units provides cells
with a wider range of functions.
Learning Objectives
LO 4.22 The student is able to construct
explanations based on evidence of how
variation in molecular units provides
cells with a wider range of functions.
[See SP 6.2]
Resources:
Presentation: click here
Textbook Reading
Campbell’s Biology- Ch. 5
Open Stax Biology- 4: Section 4.5 & 4.6, Chapter 5: Section 5.1
Biozone Volume pp. 42, 43-45 (relevant parts), 46 (relevant parts), 48-49 (relevant parts), 59-63
Supplementary Resources:
“Crash Course: Biology” Videos: In Da Club - Membranes & Transport: Biology #5
Videos from Bozemanscience: “A Tour of the Cell”, “Cellular Organelles”
Questions to answer
1. How does the structure of the cytoskeleton contribute to its function?
2. Diagram an individual phosopholipid and a bilayer of phospholipids. Label the hydrophillic head, and
hydrophobic tails in both.
3. Explain the Fluid Mosaic model of the cell membrane and describe the functions of the proteins that are
embedded in the membrane.
4. Diagram the cell membrane. Label the following parts: lipid bilayer, integral proteins, peripheral proteins,
cholesterol, cytoskeleton, extracellular matrix, glycoproteins, glycolipids. Explain the function of each part of
the cell membrane in contributing to the functioning of the cell.
5. If cells can not visually inspect other cells, how do the cells of our immune system know if a particular cell they
encounter is part of us or part of another organism?
Things you should make sure you understand: (PLEASE ask questions about them in class)







The structure and function of cilia and flagella.
The structure and functions of the three major components of the cytoskeleton (microfilaments, microtubules,
and intermediate filaments).
Why particular substances will or will not be able to pass through the phospholipid bi-layer of the cell
membrane.
How membrane-protein structure can allow for portions of the protein to be embedded in the membrane AND
allow portions to extend in to and out of the cell.
The structure and function of the cell wall.
The structure and function of the extracellular matrix.
The differences in structure and function among the types of intercellular junctions found in cells (tight
junctions, gap junctions, desmosomes, and plasmodesmata)