Bio 214 Syllabus - Fall 2020

Syllabus
BIO214 Cell Biology

Fall 2020
Instructor: Carole Gibson

Professor of Biology
Wake Forest University
gibsoncl@wfu.edu
Office hours:
Via class Zoom link.
Daily, 11:00 am – 12 pm, or by arrangement
Required books:
Essential Cell Biology by Alberts et al (fourth or fifth edition)
BIO214 Lab Book, available on Canvas in the Bio Core lab site
Learning Objectives:
Students will be able to
Explain the relationships between structure and function in the cell.

Understand the way cells acquire and use energy, and the principles that govern these
processes.
Apply the understanding of the ways that cells use energy to the concept of movement of
cells and of molecules and structures within cells.
Describe the signaling processes that regulate communication between cells and their
environment.
Correlate the effects of loss of specific enzyme function due to environmental factors or
mutation to known human diseases.
Learn how cell biologists conduct and interpret experiments.
Design experiments based on foundational knowledge of the methods and tools of cell
biology.
Structure of course:
There are two or three videos to be viewed each week, and as well as assigned readings.
Each student is assigned to a discussion group that meets synchronously either Monday,
Wednesday or Friday at 10 am on Zoom. Attendance at these sessions is required.
Each student will complete a short multiple choice quiz before his or her live session.
Participation in the class or online discussion contributes to the discussion grade, which is 20%
of the final grade.
Class Zoom link:
https://wakeforest-university.zoom.us/j/93591510877?
pwd=Wk8xTU55ejAxRjUrL1kzS1pwZVZ0UT09
password 777436
Rules and expectations:

Turn off your phones during scheduled class times. Cell phone usage during a quiz or an exam
will be considered an honor violation.
Students must take all exams and quizzes at the scheduled time unless there is a medical or
Dean’s excuse.
Academic Integrity
The Wake Forest Honor Code states, "Each student is pledged to be trustworthy in all matters ...
a student pledges in all phases of life, not to cheat, plagiarize, engage in other forms of
academic or social misconduct, deceive or steal." [See the current WFU Student Handbook]. If
you are aware of any student who performs an act of academic dishonesty, you must report it to
the instructor.
Academic dishonesty results in referral to the Honor Council and/or a grade of F in the course.
GRADING
Category % of Overall Grade

Quizzes 25%
Grading scale:
Participation/attendance at live 20%
A 94% - 100% A- 90% - 93%
sessions
B+ 86% - 89% B 83% - 85%
Exams (midterm/final) 30%
B- 80% - 82%
Lab 25% C+ 76% - 79% C 73% - 75%
C- 70% - 72%
D+ 66% - 69% D 63% - 65% D- 60% - 62%
F 59% and below
Student Support Resources
The Current Students webpage provides links to many of the resources available to you.
Here are direct links to some of the support services that you might find particularly useful.
 The Learning Assistance Center - Contact this office if you have a disability and require
accommodations.
 ZSR Library - Much of the library’s content and all of their services are available even when you
are at a distance. This includes the ability to chat directly with a librarian!
 University Counseling Center
 Office of Academic Advising
 Office of Financial Aid
SUMMARY SCHEDULE
MODULE WEEK OF READING VIDEOS
0 Aug 26 Welcome Video
1 Aug 31 Chapter 1 1-2. How we study cells

1-3. Prokaryotic and eukaryotic cells
2 Sept 7 Chapter 2 2-1. Chemical bonds and small molecules (optional)

2-2. Macromolecules
3 Sept 14 Chapter 3 3-1. Energy and catalysis

Chapter 4 3-2. Protein structure
4. Sept 21 Chapter 4 4-1. How proteins work

4-2. How proteins are studied
5. Sept 28 Chapter 11 5-1. Membrane structure

Chapter 12 5-2 Transport across membranes
6. Oct 5 Chapter 13 6-1. How cells obtain energy from food

6-2. Glycolysis and the citric acid cycle
Oct 12 MIDTERM EXAM (oral)
7. Oct 19 Chapter 14 7-1. Energy generation in mitochondria

7-2. Energy generation in chloroplasts
8. Oct 26 Chapter 15 8-1. Membrane-enclosed organelles and protein sorting

8-2. vesicular transport and endocytic pathways
9. Nov 2 Chapter 16 9-1. Cell signaling/ G protein coupled receptors

9-2. Enzyme-coupled receptors
10. Nov 9 Chapter 17 10-1. Cytoskeleton/microtubules

10-2. Cytoskeleton/actin filaments
11. Nov 16 Chapter 18 11-1. The cell cycle control system

11-2. Mitosis and meiosis
Nov 23 Thanksgiving
12. Nov 30 Chapter 20 12-1 Tissues/extracellular matrix

12-2. Cancer
Dec 6 FINAL EXAM (oral)
DETAILED SYLLABUS
MODULE 0 – week of August 26
Welcome
Video 1-1 Welcome

Live sessions All students 10 am Wednesday August 26 and Friday August 28
Zoom link https://wakeforest-university.zoom.us/j/93591510877?
MODULE 1 – week of August 31

Introduction to cells
Learning Objectives
Summarize the properties of cells.
Contrast prokaryotic and eukaryotic cells.
Explain the structure of viruses and prions, and understand how each functions as an infectious
agent.
Describe the different types of microscopy and the uses of each.
List the functions of the membrane-bound organelles in eukaryotic cells.
Argue that mitochondria and chloroplasts evolved from free-living prokaryotes.
Understand the importance of model systems in cell biology.
Videos 1-1 How we study cells

1-2 Prokaryotic and eukaryotic cells
Reading Essential Cell Biology – chapter 1
Quiz 1 To be completed by live session
Online Discussion: Express yourself! Do you have any content questions you would like to pose to the
group? Was there anything that was unclear to you? Or, you can answer a posted question by explaining
an unclear concept! Have you read anything outside of the assigned readings relevant to this week’s
content that you could share? Or any cool articles relevant to cell biology in general? Any Covid-19
updates?
Live session Group A - Monday August 31

Group B - Wednesday September 2
Group C – Friday September 4

password 777436
Module 2. Week of September 7 – Chemical Components of Cells
Learning Objectives
Explain how the different types of chemical bonds are formed and differentiate between them in
terms of their electronic configuration, strength and stability.
Identify what determines the polarity of a chemical bond and summarize its consequences for the
solubility and hydrophobicity of a molecule, and its ability to act as an acid or base.
Demonstrate how acids and bases cooperate to maintain the pH of cells.
Contrast hydrogen bonds, electrostatic attractions, van der Waal’s attractions, and the
hydrophobic force in terms of how and when they form and the role they play in the cell.
Express how the chemical and physical properties of functional groups influence the behavior of
molecules in which these groups typically occur.
Illustrate how the processes of condensation and hydrolysis are central to the synthesis and
breakdown of the large organic molecules from sets of smaller organic building blocks.
Describe a sugar and relate the different roles that they can play in the cell.
Summarize what makes amino acids chemically unique and categorize the 20 amino acids
commonly found in proteins on the basis of their chemical properties.
Explain how weak, noncovalent bonds can lead to strong and specific associations between
macromolecules or between an enzyme and its substrate.
Describe the structures and functions of proteins, lipids and carbohydrates.
Draw the subunit molecules of the proteins, lipids and carbohydrates, and illustrate how each
assembles into macromolecules.
Videos 2-1 Chemical bonds and small molecules (optional)

2-2 Macromolecules
Reading Chapter 2 Essential Cell Biology
Online Discussion
Live session Group A 10 am Monday September 7

Group B 10 am Wednesday September 9
Group C 10 am Friday September 11
password 777436
Module 3 – Week of September 14

Energy and Catalysis
Protein structure
Learning Objectives: Energy and Catalysis

Describe the first and second law of thermodynamics, and their significance to understanding
metabolic reactions
State how living systems can generate and maintain order without violating the second law of
thermodynamics.
Summarize how living systems take advantage of the first law of thermodynamics.
Express why sunlight provides the ultimate source of energy for nearly all living things.
Contrast photosynthesis and cellular respiration and evaluate how the processes complement
one another.
Differentiate between oxidation and reduction in terms of the movement of electrons, protons,
and oxygen atoms.
Recall the relationship between the free energy change and the entropy change of the universe.
Articulate how enzymes increase the speed of a chemical reaction.
Relate how the free-energy change of a reaction determines its energetic favorability.
Review the relationship between /G, equilibrium, and the concentrations of a reaction’s
substrates and products.
Relate /G to /G0.
Formulate how the equilibrium constant, K, governs the direction of a reaction and the amount
of product it generates.
Explain how the pathway that converts sugars into CO 2 and H2O proceeds rapidly to completion
despite the fact that several of its constituent reactions are energetically unfavorable.
Summarize how substrate concentration affects an enzyme’s activity.
Describe how noncovalent interactions allow enzymes to interact with specific substrates.
Explain why substrates for different enzymes can coexist in the same compartment.
Illustrate how enzymes affect the equilibrium point of chemical reactions.
Review how activated carriers link catabolic and anabolic reactions.
Evaluate why ATP hydrolysis has such a large negative /G0 and an even larger negative /G.
Relate how the energy of ATP hydrolysis can be harnessed to drive an energetically unfavorable
condensation reaction.
Delineate the role played by NADPH in oxidation–reduction reactions.
State why the oxidation of NADPH is energetically favorable.
Name 3 activated carriers and state the role each plays in a cell.
Evaluate the energetic favorability of condensation and hydrolysis reactions and state which
type of reaction generally requires linkage to ATP hydrolysis to occur.
Outline how ATP hydrolysis provides the energy needed for highly unfavorable reactions, such
as the biosynthesis of nucleic acids
Learning Objectives: Protein structure

Explain how noncovalent interactions—including electrostatic attractions, hydrogen bonds, van
der Waals attractions, and hydrophobic forces—influence the shape of a folded protein and
how the polypeptide backbone and amino acid side chains participate in these interactions.
Explain how chaperone proteins guide the folding of a polypeptide chain—and why some
proteins can fold without chaperone assistance.
Contrast the hydrogen bonding patterns that give rise to alpha helices with those that produce
beta sheets.
Describe the role that protein domains play within a protein’s three-dimensional structure.
Define a protein’s primary, secondary, tertiary, and quaternary structures.
Compare how covalent crosslinks and noncovalent bonds help to establish protein structure.
Summarize the roles that noncovalent interactions and exact protein conformation play in
allowing proteins to recognize and bind specifically to their ligands.
Explain how antibodies, which share the same basic structure, can recognize a limitless diversity
of antigens.
Explain the significance of an enzyme’s Michaelis constant, KM, and explain how this value
influences which biochemical pathway a substrate might follow.
Describe how enzymes can reduce the activation energy needed to catalyze chemical reactions.
Explain how the binding of a ligand at a regulatory site can alter the activity of a protein or
enzyme.
Explain how chemical modification such as phosphorylation can influence a protein’s function
Contrast how protein activity is regulated by phosphorylation or by the binding of nucleotides
such as GTP or ATP.
Videos 3-1. Energy and catalysis

3-2. Protein structure

Chapter 4 p 117 - 136
Online Discussion

password 777436
MODULE 4 – WEEK OF SEPTEMBER 21

Proteins (continues from Module 3)
Learning Objectives
How proteins work:
Summarize the roles that noncovalent interactions and exact protein conformation play in
allowing proteins to recognize and bind specifically to their ligands.
Explain how antibodies, which share the same basic structure, can recognize a limitless diversity
of antigens.
State the significance of an enzyme’s Michaelis constant, KM, and explain how this value
influences which biochemical pathway a substrate might follow.
Describe how enzymes can reduce the activation energy needed to catalyze chemical reactions.
Explain how and why different forms of feedback control might be used to regulate enzyme
activity.
Explain how the binding of a ligand at a regulatory site can alter the activity of a protein or
enzyme.
Explain how chemical modification such as phosphorylation can influence a protein’s location
and interactions.
Contrast how protein activity is regulated by phosphorylation or by the binding of nucleotides
such as GTP or ATP. Explain how the hydrolysis of ATP or GTP can produce the
directional movement of motor proteins or coordinate the activity of large protein
machines.
Describe how scaffold proteins aid in the assembly of protein complexes.
Explain how intracellular condensates can form biochemical subcompartments in a cell.
How proteins are studied:

Compare the three types of column chromatography, and explain when each might be best used
Contrast chromatography and electrophoresis as methods for protein separation.
Describe how the existence of protein families affects the determination of protein structure.
Videos 4-1. How proteins work

4-2 How proteins are studied
Reading Chapter 4 Essential Cell Biology p 137-158

Quiz 4 To be completed before live session
Online Discussion


password 777436
MODULE 5 – WEEK OF SEPTEMBER 28 – Membrane structure and transport
Learning Objectives: Membrane structure

Articulate how the amphipathic nature of membrane lipids drives the assembly of a lipid bilayer,
as well as the formation of closed vesicles, organelles, and even whole cells.
Explain why fats such as triacylglycerol coalesce into fat droplets in water.
Recall the structures of phospholipids, glycolipids, triacylglycerol, and cholesterol.
Summarize how the length and saturation of lipids’ hydrophobic tails affect the fluidity of a cell
membrane.
State how the inclusion of cholesterol affects the permeability of animal cell membranes.
Propose how single-celled organisms such as yeast and bacteria can maintain the fluidity of their
membranes as temperatures rise and fall.
Review the reasons why cells carefully regulate their membrane fluidity.
State where new phospholipids are produced and explain how membranes are able to grow
evenly.
Outline how the asymmetric distribution of phospholipids, characteristic of different membrane
types, is established and maintained.
Describe how membranes retain their orientation during transfer between cell compartments.
Contrast the actions of flippases and scramblases.
Compare the relative mass and number of protein and lipid molecules in a typical animal cell
membrane.
List some functions of plasma membrane proteins.
Distinguish between integral membrane proteins and peripheral membrane proteins.
Explain how the polypeptide chain of a transmembrane protein, with its hydrophilic backbone, is
able to span the hydrophobic interior of the lipid bilayer.
Contrast the structure and potential function of single-pass and multipass transmembrane
proteins.
Describe the structure of a membrane-spanning β-barrel transmembrane protein.
Relate the structure and function of the membrane protein bacteriorhodopsin.
Contrast how the plasma membrane is mechanically stabilized in animal cells versus plant cells.
Explain how hybrid cells allowed investigators to monitor the movement of membrane proteins
within the plane of the lipid bilayer.
Describe how fluorescence recovery after photobleaching (FRAP) allows investigators to assess
membrane fluidity.
Outline the ways that cells restrict the lateral movement of their membrane proteins.
Review the structure and function of the glycocalyx.
Learning Objectives: Membrane transport

Distinguish between simple diffusion and facilitated transport.
State the function of membrane transport proteins and differentiate between transporters and
channels.
Indicate how the concentration of ions in the cell differs from that outside the cell.
Compare how transporters and channels discriminate among solutes, moving only a select
subset across the membrane.
Distinguish between active and passive transport, and indicate which type of membrane
transport protein carries out each.
Review the forces that govern the passive transport of charged and uncharged solutes across a
cell membrane.
Compare the electrochemical gradients for sodium and potassium ions, and recall how the
membrane potential and concentration gradient for each ion combine to influence its
movement across the plasma membrane.
Describe the ways in which water can move across cell membranes, and articulate what governs
whether water will enter or exit a cell.
Contrast how plant cells, animal cells, and protozoa maintain their osmotic equilibrium.
Outline how the glucose transporter in the plasma membrane of mammalian cells imports
glucose after a meal and exports glucose to provide fuel for other tissues in the body.
List three sources of energy used by transmembrane pumps to actively transport a solute
against its concentration gradient.
Review how the sodium pump in animal cells uses the energy supplied by ATP hydrolysis to
maintain the concentration gradients of sodium and potassium ions.
Explain why—and how—cells keep the cytosolic concentration of calcium ions low.
Differentiate between a symport, an antiport, and a uniport.
Compare the uniport glucose transporter and the glucose-sodium symport in terms of their
activities and roles in glucose transport in intestinal epithelial cells.
Express how the sodium—proton exchanger in the plasma membrane allows animal cells to
control the pH of their cytosol.
Review how proton pumps provide the energy for the transport of solutes in plants, fungi, and
bacteria.
Explain how the structure of ion channels leads to their ion selectivity.
Outline how patch-clamp recording can be used to study the activity of ion channels.
Review the mechanisms that can regulate ion flow through a channel.
Define “gating” and list the types of conditions that can alter the opening and closing of ion
channels.
Summarize the process by which ion channels in auditory hair cells allow the detection of sound.
List several cell types that use voltage-gated ion channels.
Explain how voltage sensors allow voltage-gated ion channels to respond to changes in
membrane potential.
Videos 5-1. Principles of membrane transport

5-2. Transport across cell membranes
Quiz 5 To be completed during live session
Online discussion

Group C 10 am Friday September Oct 2

password 777436
MODULE 6 – WEEK OF October 5
Objectives
Define cell respiration.
List three categories of food molecules that can serve as energy sources for cells, and identify
the sugar whose breakdown generates most of the energy produced by the majority of
animal cells.
Summarize why cells need enzymes to maximize the energy that can be harvested from the
oxidation of a fuel molecule such as glucose.
Outline the three stages of catabolism, indicating where each takes place and identifying the
stage’s major products.
Recall the efficiency with which energy released from the oxidative breakdown of sugars and
fats is captured by cells.
Summarize the amount of ATP energy invested and the amount recouped during the
breakdown of a glucose molecule during glycolysis.
List the end products of glycolysis.
Explain why energy is released by the splitting of glucose into pyruvate during glycolysis.
Present the reactions by which ATP is generated by substrate-level phosphorylation
List enzyme types involved in glycolysis and indicate their functions.
Recall how the generation of NADH in glycolysis is linked to an oxidation reaction.
Describe the consequence of phosphorylating glucose in the first step of glycolysis.
Contrast the fermentation pathway in an oxygen-starved muscle cell with the pathway in a yeast
cell that is growing anaerobically.
Identify the products that would build up in the cytosol if glycolysis were to take place in the
absence of oxygen in cells that cannot carry out fermentation.
Recall why—and in which step—glycolysis would halt in the absence of oxygen in cells that
cannot carry out fermentation.
Contrast anaerobic respiration with fermentation.
Explain what it means for a bond to be described as having “high energy.”
Explain how the generation of 1,3-bisphosphoglycerate in step glycolysis drives the production
of ATP
Summarize how the pyruvate produced by glycolysis is converted into acetyl CoA, and state
where the process takes place.
Review how and where the fatty acids derived from fat are converted into acetyl CoA.
Recall where glycolysis and acetyl CoA production take place in aerobic prokaryotes.
Explain why oxygen is required for the citric acid cycle to continue.
Recount where the oxygen used during the oxidation of glucose to carbon dioxide ultimately
goes.
Identify the origin of the oxygen atoms used during the citric acid cycle to produce carbon
dioxide.
State where the citric acid cycle takes place in animal cells, in plant cells, and in prokaryotes.
Outline the fate of the acetyl group carbons that enter the citric acid cycle.
List the activated carriers produced for each molecule of acetyl CoA that enters the citric acid
cycle.
Describe the role of oxaloacetate in the citric acid cycle.
Review how intermediates of glycolysis and the citric acid cycle can be used to synthesize other
molecules needed by the cell.
Summarize how oxygen is used by the electron transport chain.
Compare the number of ATP molecules generated by glycolysis with the number produced by
the complete oxidation of glucose to water and carbon dioxide.
Outline briefly how the energy captured during glycolysis and the citric acid cycle is used to
generate ATP
Videos 6-1. How cells obtain energy from food

6-2. Glycolysis and the citric acid cycle
Online discussion
Live session Group A 10 am Monday October 5

Group B 10 am Wednesday October 7
Group C 10 am Friday October 9

password 777436
Objectives
Identify the molecule that serves as the main source of chemical energy in a cell.
Differentiate between the mechanisms of ATP production by glycolysis and by oxidative
phosphorylation.
Summarize the membrane-based processes involved in oxidative phosphorylation and
photosynthesis.
Summarize the stages involved in generating ATP by oxidative phosphorylation.
List the evidence suggesting that both mitochondria and chloroplasts evolved from bacteria that
were engulfed by ancestral cells.
State the percentage of the free energy available in a molecule of glucose that is captured
during glycolysis, and relate that efficiency with that of a gasoline-powered engine.
Review the consequences of disrupting electron transport in mitochondria.
Explain how mitochondrial replacement therapy can be used to prevent the transmission of
mitochondrial defects.
Compare where mitochondria are located in a heart muscle cell, sperm, and fibroblast.
Recall how many mitochondria are present in a typical cell and how their numbers can change
with the energy needs of the cell.
Describe the structure of a mitochondrion and distinguish the functions and compositions of its
different membranes and compartments.
Review how pyruvate and fatty acids move from the cytosol to the mitochondrial matrix, and
identify the metabolic intermediate into which both are converted before entering the
citric acid cycle.
Recall the activated carriers, generated by the citric acid cycle, that will transfer high-energy
electrons to the electron transport chain.
Outline the process that allows much of the energy contained in the high-energy electrons of
activated carriers to be stored in the high-energy phosphate bonds of ATP.
Distinguish the source of the high-energy electrons that power ATP production during cell
respiration and photosynthesis.
List the components of the electron transport chain in their order of operation, including mobile
electron carriers, and describe the functions of each.
Compare the electron affinities of the components of the electron transport chain, and describe
the change in energy of electrons as they move along the chain.
Recall the direction in which protons are pumped across the inner mitochondrial membrane and
describe the resulting pH difference in the mitochondrial matrix and intermembrane
space.
Review the membrane potential and pH gradients across the inner mitochondrial membrane,
and state in which direction it is energetically favorable for protons to flow.
Explain how ATP synthase acts as a motor to convert the energy of protons flowing down an
electrochemical gradient into the chemical bond energy in ATP.
Describe the conditions under which ATP synthase will act as a proton pump and hydrolyze ATP.
Outline how the electrochemical proton gradient is used to drive the transport of metabolites
across the inner mitochondrial membrane in eukaryotic cells and to power the rotation
of flagella in motile bacteria.
Compare where electrons donated by NADH and FADH 2 enter the respiratory chain, and relate
how much ATP is ultimately produced by each activated carrier.
Identify the main source of the protons that are pumped across the inner mitochondrial
membrane by the electron transport chain.
Summarize how electron carriers are able to transfer a proton from one side of the membrane
to the other.
Relate redox potential to electron affinity and describe how the redox potentials of
reduced/oxidized nicotinamide adenine dinucleotide and oxygen/water align with their
functions in the respiratory chain.
Estimate the number of ATP molecules that could be synthesized from the energy released by
the transfer of two electrons from NADH to molecular oxygen.
Explain why NADH does not donate its electrons directly to molecular oxygen in living systems.
Compare the redox potentials of components in the electron transport chain and state which
way electrons will flow.
Identify the metals that help give cytochrome c oxidase its high redox potential.
Name the atoms or molecules that are oxidized or reduced by cytochrome c oxidase.
Summarize why cytochrome c oxidase must bind oxygen tightly.
Outline how conformational change in cytochrome c oxidase pumps protons across the inner
mitochondrial membrane.
Outline how investigators used an artificial system including bacteriorhodopsin and ATP
synthase to demonstrate the role that a proton gradient plays in producing ATP.
Describe the structure of a chloroplast and indicate the functions of its membranes and
compartments, including where chlorophyll and the photosynthetic machinery are
contained.
Outline the events that take place during stage 1 of photosynthesis and compare this process to
the oxidative phosphorylation that occurs in mitochondria.
Review the events that take place in stage 2 of photosynthesis and indicate where these
reactions occur.
Recall the wavelengths of light that are absorbed or reflected by chlorophyll.
Delineate the functions of chlorophyll’s porphyrin ring and hydrophobic tail.
List the components of a photosystem.
Summarize how light energy, captured by a chlorophyll molecule in an antenna complex, gets
transferred to the chlorophyll special pair in the reaction center.
Outline how the transfer of an electron from the chlorophyll special pair to a mobile electron
carrier creates a charge separation that effectively converts light energy into chemical
energy.
Differentiate between photosystems I and II, indicate the electron carriers to which they
transfer their high-energy electrons, and state the source of the electrons that replace
those donated by their chlorophyll special pairs.
Name the components of the photosynthetic electron transport chains and describe their
functions.
State what drives the production of ATP by ATP synthase during photosynthesis.
Identify the component of the photosynthetic machinery that generates all of the oxygen we
breathe.
Explain how the photosynthetic machinery produces enough energy to remove electrons from
water and uses them to produce NADPH.
Identify the molecules that provide the energy to convert carbon dioxide into sugars.
Describe the role that ribulose 1,5-bisphosphate plays in the carbon fixation cycle.
Name the three-carbon product of carbon fixation and state how many molecules of ATP and
NADPH are required for its synthesis.
Review how the products of photosynthesis feed into oxidative phosphorylation—and vice
versa.
Videos 7-1. Energy generation in mitochondria

7-2. Energy generation in chloroplasts
Online discussion
Live session Group A 10 am Monday October 19

Group B 10 am Wednesday October 21
Group C 10 am Friday October 23

password 777436
Objectives
List the major membrane-enclosed organelles of the eukaryotic cell and briefly describe the
function of each.
Identify the eukaryotic organelles that are surrounded by double membranes.
Describe the relationship between the ER and the nuclear membrane.
Compare the functions of rough ER and smooth ER, and describe the types of cell in which each
can be found.
List the organelles that form the endomembrane system and review how the interiors of these
organelles communicate with one another and with the cell exterior.
Contrast the evolution of the nucleus with that of mitochondria and chloroplasts.
Outline the mechanisms by which proteins can enter membrane-enclosed organelles, and
identify the organelles that use them.
List the membrane-bound organelles that can receive proteins directly from the cytosol.
Describe the fate of proteins that lack a sorting signal.
Review where the proteins found in mitochondria and chloroplasts are synthesized.
Relate what would happen if an ER signal sequence were removed from an ER protein and
attached to a cytosolic protein.
Predict what would happen to a protein that bears both a nuclear localization signal and a
nuclear export signal.
Describe the structure of the nuclear envelope.
Contrast the conformation adopted by proteins during nuclear transport and that of proteins
transported into mitochondria and chloroplasts.
Explain how nuclear pores restrict the passage of larger molecules while allowing small, water-
soluble molecules to pass freely between the nucleus and cytosol.
Review how nuclear import receptors escort proteins bearing a nuclear localization signal from
the cytosol into the nucleus.
Describe the types of molecules transported by nuclear export receptors.
Articulate how mitochondrial proteins are recognized and transported into the mitochondrial
matrix, and describe the role played by chaperones inside the organelle.
Name the organelle that serves as an entry point for proteins destined for all organelles or for
the cell surface.
Distinguish between free ribosomes and membrane-bound ribosomes.
Identify the source of energy for the transport of proteins into the ER.
Compare a polyribosome and the rough ER.
Review how the signal-recognition particle (SRP) and SRP receptor guide proteins containing an
ER signal sequence to the ER membrane.
Recall the location, functions, and ultimate fate of the ER signal sequence on soluble proteins.
Compare the locations and fates of the ER signal and stop-transfer sequences of single-pass
transmembrane proteins to the start-transfer and stop-transfer sequences of multipass
transmembrane proteins.
Contrast the endocytic and exocytic pathways in terms of directionality, purpose, and
participation of certain organelles and membranes.
Recall the function and fate of the protein coat that surrounds transport vesicles.
Summarize how clathrin-coated vesicles select their cargo molecules and then bud from their
parent membranes.
Compare the processes of vesicle tethering, docking, and fusion, and list the proteins involved in
each
List the types of covalent modifications that take place in the ER and describe the functions
these modifications serve.
Review how proteins are selected for glycosylation in the ER and how these sugars are attached
to the protein.
Recall how proteins destined to function in the ER are kept in the ER—or returned to the ER if
they accidentally enter the Golgi apparatus.
Summarize how misfolded or not fully assembled proteins are retained in the ER.
Explain the unfolded protein response and outline the consequences of triggering this program.
Describe the structure and location of the Golgi apparatus.
Articulate the ways in which proteins move from one cisterna to another within the Golgi
apparatus.
Compare how proteins are sorted in the cis and trans Golgi networks.
Recall how and where additional oligosaccharides are added to glycoproteins within the Golgi
stack.
Contrast the constitutive and regulated exocytosis pathways, and describe the behavior of the
proteins secreted by each pathway
Explain how GFP can be used to monitor the location and movement of proteins in living cells.
Distinguish between pinocytosis and phagocytosis, and indicate the types of cells that engage in
each.
Describe how cholesterol is transported into the cell cytosol by receptor-mediated endocytosis.
Summarize how viruses take advantage of receptor-mediated endocytosis.
Outline the possible fates of receptor proteins and cargo molecules following endocytosis into
endosomes.
Recall how endosomes maintain their pH and explain how pH plays a crucial role in the
endosomal sorting process.
Recall how lysosomes maintain their pH and describe the role that pH plays in lysosomal
function.
List the types of enzymes present in lysosomes and summarize how these enzymes are
transported into lysosomes.
Outline the pathways that different materials follow to arrive in lysosomes.
Describe autophagy and explain when or why cells might use this pathway.
Videos 8-1. Membrane-enclosed organelles

8-2. Protein sorting and vesicular transport
Online discussion
Live session Group A - Monday October 26

Group B - Wednesday October 28
Group C – Friday October 30

password 777436
MODULE 9 – WEEK OF November 2
Objectives
Distinguish the main types of signal-mediated cell—cell communication and identify the type of
extracellular signal molecule involved in each.
Outline the main classes of extracellular signal molecules, and describe the types of receptors to
which they bind.
Explain how the same signal molecule can induce different responses in different target cells.
Recall how a combination of signals can evoke a response that is different from the sum of the
effects that each signal can trigger on its own.
Differentiate the types of cell responses that occur rapidly with those that take minutes or hours
to execute.
Name the basic components needed for an extracellular signal molecule to change the behavior
of a target cell, and identify the site at which the primary step in signal transduction
takes place.
Summarize how phosphorylation can act as a molecular switch, and identify the types of
proteins that add and remove this chemical modification.
Distinguish the two main types of GTP-binding proteins.
Describe how monomeric GTPases toggle between active and inactive forms.
Differentiate the three main classes of cell-surface receptors and provide an example of each.
List some foreign substances that alter physiology by interacting with cell-surface receptors.
Describe the type of signal transduction carried out by ion-channel-coupled receptors.
Review the structure of G-protein-coupled receptors (GPCRs) and describe the types of
extracellular signal molecules that bind to them.
Recall the general structure of a G protein and describe how the protein responds when
activated by a GPCR.
Summarize the factors that determine the duration of a GPCR-stimulated response.
Contrast how cholera toxin and pertussis toxin exert their effects.
Relate the speeds of the responses produced by G proteins activating an ion channel versus
activating a membrane-bound enzyme.
Name the classes of enzymes that are the most frequent targets of G proteins, and list the
second messenger molecules they produce.
Outline how cyclic AMP is produced in response to G protein activation, and recall how caffeine
can potentiate this response.
Compare a signaling pathway in which cyclic AMP produces a response within seconds to one in
which the response takes minutes or hours to develop.
Recall the location and action of the second messenger molecules produced by activated
phospholipase C.
List several biological processes triggered by calcium ions.
Explain how cells keep the concentration of calcium ions in the cytosol low and how they
terminate a calcium ion signal.
Review how calcium-responsive proteins such as calmodulin propagate a calcium ion signal.
Outline how the gas nitric oxide (NO) can act as a signaling molecule to trigger the relaxation of
smooth muscle cells.
Recall why nitric oxide acts as a paracrine signal only on cells near its site of synthesis.
Outline how GPCRs in the photoreceptors of the retina transmit an extremely rapid signal in
response to stimulation by light.
Summarize how adaptation in the intracellular signaling cascade of photoreceptors allows the
eye to respond to dim or bright light.
Compare the general structures of GPCRs and enzyme-coupled receptors such as receptor-
tyrosine kinases (RTKs).
Review how the binding of a signal molecule activates RTKs to trigger the assembly of an
intracellular signaling complex.
Recall how signals transmitted by RTKs can be terminated.
List several intracellular signaling proteins activated by RTKs.
Outline how RTKs activate the MAP kinase signaling module.
Indicate how Ras can fuel uncontrolled proliferation in cancer.
Review how different types of receptors can trigger a rise in the cytosolic concentration of
calcium ions.
Review how a technology such as RNA interference or CRISPR can be used to assess the
importance of a particular protein in a signaling pathway.
Explain how mutant proteins can be used to determine the order in which proteins participate in
a signaling pathway.
Outline how steroid hormones trigger the transcription of different sets of target genes.
Explain how multiple signaling pathways can integrate information to produce a coordinated cell
response.
Videos 9-1. Cell signaling/ G protein coupled receptors

9-2. Enzyme-coupled receptors
Reading Chapter 16
Online discussion
Live session Group A - Monday November 2

Group B - Wednesday November 4
Group C – November 6

password 777436
Objectives
Contrast the structures of the subunits that form intermediate filaments, actin filaments, and
microtubules.
Describe the location and main function of intermediate filaments.
Recall how the structure of intermediate filaments relates to their strength and durability.
Summarize how intermediate filaments are assembled and describe their polarity.
Review how intermediate filament proteins can differ from one another and how these
differences relate to the function of the intermediate filament.
Describe three disorders that involve defects in intermediate filaments.
Compare the structure of the nuclear lamina with that of cytoplasmic intermediate filaments.
Review how the nuclear lamina disassembles and re-forms during each cell division.
Recall how intermediate filaments are stabilized by cross-linking accessory proteins, and explain
how these proteins help to position the nucleus within the cell interior.
Review the general location and functions of microtubules.
List several examples of organizing centers from which microtubules grow.
Describe the structure of microtubules and recall how microtubules are assembled from tubulin
dimers.
State the polarity of a microtubule and summarize how this polarity affects its assembly and
function.
Describe the structure of a centrosome and review how the centrosome nucleates the growth of
microtubules.
Describe dynamic instability and indicate how this behavior relates to microtubule function.
Summarize how dynamic instability is controlled by GTP hydrolysis.
Contrast the actions of colchicine and Taxol and explain why both are used to treat human
cancers.
Compare kinesins and cytoplasmic dyneins in terms of their structure, their movement along the
microtubule, and how they interact with cargo.
Compare the roles that kinesins and cytoplasmic dyneins have in positioning the organelles in a
eukaryotic cell.
Summarize how fluorescent marker proteins and non-hydrolyzable ATP analogs can be used to
study the activity of motor proteins such as kinesin or myosin.
Compare the functions and movements of cilia and flagella.
Describe the arrangement of microtubules inside a cilium or flagellum.
Outline how ciliary dynein allows a cilium to bend.
List several cell structures formed by actin filaments.
Compare actin filaments and microtubules in terms of width, length, polarity, and cross-linking.
Compare the polymerization of actin filaments to that of microtubules.
Explain treadmilling and identify the conditions under which this behavior takes place.
Compare the actions of cytochalasin and phalloidin and describe their effects on cell behavior.
Outline the functions of common actin-binding proteins
Differentiate between lamellipodia and filopodia.
Distinguish the roles played by actin in the protrusion, attachment, and contraction involved in
cell movement.
Explain how ARPs and formins aid in the assembly and extension of protrusions at the cell’s
leading edge.
Summarize how different members of the Rho family of GTPases alter the organization of actin
filaments.
Compare the structure, binding properties, and general function of myosins I and II.
Videos 10-1. Cytoskeleton/microtubules

10-2 Actin filaments
Reading Chapter 17
Online discussion

password 777436
Objectives
List the four phases of the eukaryotic cell cycle and summarize what takes place in each.
Identify the phases that are shortened during the cleavage divisions of early embryos, and
explain the effects of these divisions on cell size.
Summarize the function of the cell-cycle control system and describe the transition points at
which progression through the cycle is regulated.
Explain how studies of yeast can lead to insights into the biology of human cancers.
Compare how cyclins and Cdks vary in concentration and activity during the cell cycle.
Recall why different cyclin-Cdk complexes trigger different events in the cell cycle.
Explain how extracts prepared from cells in different phases of the cell cycle have been used to
identify components of the cell-cycle control system.
Explain how studies of mutant yeast were used to dissect the cell-cycle control system.
Describe how the synthesis and destruction of cyclins regulate progression from one phase of
the cell cycle to the next.
Recall how dephosphorylation helps trigger the abrupt activation of cyclin-Cdk complexes.
Indicate how Cdk inhibitors can help regulate progression through the cell cycle.
Summarize the mechanisms that allow cells to either pause or continue through different
transition points in the cell cycle.
Review how cyclin-Cdk complexes are inhibited as cells enter G 1.
Explain how Rb blocks cell proliferation and how mitogens reverse this inhibition.
Review how DNA damage can arrest cells in G1.
State what occurs when the DNA damage detected in G 1 is too extensive to be repaired.
Contrast the arrested state G0 with the cell-cycle withdrawal that occurs during terminal
differentiation.
Indicate which phases of the cell cycle vary the most in length to influence the rates of cell
division in the adult body.
Detail how S-Cdk initiates replication and prevents re-replication during the same cell cycle.
Summarize how incomplete or incorrect replication can arrest the cell cycle in G 2.
Explain how M-Cdk is activated at the end of G 2 and indicate why this activation is sudden and
explosive.
Compare cohesins and condensins in terms of structure, function, and how and when they
assemble onto chromosomal DNA.
Compare the mitotic spindle and contractile ring in terms of composition, location, and the role
each plays in cell division.
Outline the centrosome cycle, indicating how and when it is initiated.
Describe the structure of the mitotic spindle and explain how and when it begins to form.
Summarize how and when the nuclear envelope breaks down.
Review how chromosomes are captured by spindle microtubules, and describe the structure of
the point of attachment.
Describe the role of chromosomes in assembly of the mitotic spindle.
Explain why chromosomes align at the spindle equator during metaphase, and present
experimental evidence for this mechanism.
Summarize the molecular events that trigger the separation of sister chromatids at the start of
anaphase.
Compare the changes in the mitotic spindle that underlie chromosome segregation during
anaphase A and anaphase B, and delineate the driving forces responsible for each
process.
Explain how the spindle assembly checkpoint ensures that all chromosomes are attached to the
spindle and why this checkpoint can delay the onset of anaphase and the exit from
mitosis.
Describe how the nuclear envelope reassembles during telophase.
Define the cleavage furrow and explain how its position is determined.
Review the contractile ring in terms of its composition, assembly, and mechanism of action.
Summarize how cells change in shape and attachment throughout the cell cycle.
Explain how membrane-enclosed organelles are distributed to daughter cells during cell division.
Videos 11-1. The cell cycle control system

11-2. Mitosis and meiosis
Reading Chapter 18
Online discussion


password 777436
Objectives
Contrast the extracellular matrix and cell wall, and recall what roles these materials have in the
supportive tissues of animals and plants.
Compare, in terms of structure and composition, the cell walls found in wood and those found
in a leaf.
Describe the driving force for plant cell growth.
Review the composition of a plant cell wall and identify the role of cellulose microfibrils in this
matrix.
Differentiate between the primary and secondary cell walls.
Explain how the orientation of cellulose microfibrils in a plant cell wall influences the shape of a
plant tissue.
Outline how cellulose is produced by plant cells and how the orientation of the microfibrils is
regulated.
Compare the extracellular matrix of connective tissues such as bone or tendon to that of muscle
or epidermis.
Describe the distribution of cells in a connective tissue.
Identify the component that provides tensile strength in the connective tissues of animals, and
outline what gives different connective tissues their distinctive characteristics.
Compare the structures of collagen molecules, collagen fibrils, and collagen fibers.
Distinguish the locations and functions of fibroblasts, osteoblasts, and osteoclasts.
Outline how collagen molecules are synthesized, secreted, and assembled into fibrils.
Explain how collagen fibrils become oriented in developing tissues.
Review how integrins allow cells to attach to collagen in the extracellular matrix, and explain
how these attachments are dynamically formed and broken.
Describe the structure of glycosaminoglycans and summarize how they allow connective tissue
to resist compression.
Describe the structure of proteoglycans and outline their functions in the extracellular matrix.
Define an epithelium and describe the four main types of epithelia.
Outline the main functions common to epithelia and list some functions of specialized epithelia.
Indicate the composition of the basal lamina.
Review how epithelial sheets are polarized in structure and function.
Summarize the structure and function of tight junctions.
Distinguish adherens junctions, desmosomes, and hemidesmosones in terms of structure,
location, and function.
Compare gap junctions and plasmodesmata in terms of structure, location, and function.
Summarize how stem cells divide to produce a continuous supply of terminally differentiated
cells.
Describe the general appearance, distribution, and abundance of stem cells in an adult mammal.
Contrast how cell replacement occurs in the skin epidermis with replacement in the intestinal
epithelium.
Provide examples of stem cells that give rise to several types of differentiated cells.
Outline how different signaling mechanisms contribute to maintaining the complex organization
of a stem-cell system such as that of the intestine.
Define pluripotency and summarize how embryonic stem cells can be induced to differentiate
into a variety of cell types.
Present potential obstacles to the use of human embryonic stem cells for the replacement of
damaged tissues in disorders such as Parkinson’s disease or diabetes.
Review how induced pluripotent stem cells are produced and compare their properties to those
of embryonic stem cells.
Explain how induced pluripotent stem cells are currently being used to study human disease,
cell fate, and the development of organs.
Recall the two heritable properties that define cancer cells.
Contrast benign tumors, malignant tumors, and metastases.
Present the epidemiological evidence that supports a strong role for environmental factors in
causing human cancers.
List several environmental factors involved in promoting the development of cancer.
Outline the potential sources of mutations that could contribute to cancer.
Distinguish passenger mutations from cancer-critical or driver mutations.
Explain why cancer is most often a disease of old age.
Review how genetic instability can be produced and its role in cancer progression.
Outline how tumors evolve through repeated rounds of mutation, proliferation, and natural
selection.
Summarize the characteristics that distinguish cancer cells from normal cells and how they
provide cancer cells with a competitive advantage.
Differentiate between oncogenes and tumor suppressor genes, and outline the types of genetic
events that alter the activity of each.
Identify the key regulatory pathways that are altered in almost all human cancers.
Explain how loss of the tumor suppressor gene APC can give rise to colorectal cancer, both in
families predisposed to the condition and in patients with no family history of the
disease.
Describe how an accumulation of mutations can turn a polyp in the lining of the colon into an
invasive or metastatic cancer.
Outline how antibodies can be used to identify a protein’s binding partners, for example,
proteins that interact with tumor suppressor APC.
Review how APC regulates the activity of the Wnt signaling pathway and how inactivation of
APC drives the formation of polyps.
Recall how mutations in the gene-encoding beta-catenin can cause a similar effect as mutations
in APC.
Explain how a lack of normal cell-cycle control mechanisms or DNA damage response may help
make cancer cells particularly vulnerable to therapeutic intervention.
Summarize how the immune system can be used to help kill tumor cells.
Describe how the product of a specific oncogene can be targeted therapeutically.
Videos 12-1. Tissues/extracellular matrix

12-2. Stem cells
12-3. Cancer
Reading Chapter 20
Online discussion

Group B - Wednesday December 2
Group C – December 4

password 777436

Bio 214 Syllabus - Fall 2020

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Bio 214 Syllabus - Fall 2020

Uploaded by

Copyright:

Available Formats

Syllabus

BIO214 Cell Biology

Instructor: Carole Gibson

Explain the relationships between structure and function in the cell.

Rules and expectations:

Category % of Overall Grade

Student Support Resources

MODULE WEEK OF READING VIDEOS

0 Aug 26 Welcome Video

1 Aug 31 Chapter 1 1-2. How we study cells

2 Sept 7 Chapter 2 2-1. Chemical bonds and small molecules (optional)

3 Sept 14 Chapter 3 3-1. Energy and catalysis

4. Sept 21 Chapter 4 4-1. How proteins work

5. Sept 28 Chapter 11 5-1. Membrane structure

6. Oct 5 Chapter 13 6-1. How cells obtain energy from food

Oct 12 MIDTERM EXAM (oral)

7. Oct 19 Chapter 14 7-1. Energy generation in mitochondria

8. Oct 26 Chapter 15 8-1. Membrane-enclosed organelles and protein sorting

9. Nov 2 Chapter 16 9-1. Cell signaling/ G protein coupled receptors

10. Nov 9 Chapter 17 10-1. Cytoskeleton/microtubules

11. Nov 16 Chapter 18 11-1. The cell cycle control system

12. Nov 30 Chapter 20 12-1 Tissues/extracellular matrix

Video 1-1 Welcome

MODULE 1 – week of August 31

Videos 1-1 How we study cells

Reading Essential Cell Biology – chapter 1

Quiz 1 To be completed by live session

Live session Group A - Monday August 31

Zoom link https://wakeforest-university.zoom.us/j/93591510877?

Videos 2-1 Chemical bonds and small molecules (optional)

Reading Chapter 2 Essential Cell Biology

Quiz 2 To be completed by live session

Live session Group A 10 am Monday September 7

Module 3 – Week of September 14

Learning Objectives: Energy and Catalysis

Learning Objectives: Protein structure

Videos 3-1. Energy and catalysis

Reading Chapter 3 Essential Cell Biology

Quiz 3 To be completed by live session

Live session Group A 10 am Monday September 14

MODULE 4 – WEEK OF SEPTEMBER 21

How proteins are studied:

Videos 4-1. How proteins work

Reading Chapter 4 Essential Cell Biology p 137-158

Live session Group A 10 am Monday September 21

Zoom link https://wakeforest-university.zoom.us/j/93591510877?

MODULE 5 – WEEK OF SEPTEMBER 28 – Membrane structure and transport

Learning Objectives: Membrane structure

Learning Objectives: Membrane transport

Videos 5-1. Principles of membrane transport

Reading Chapter 12 Essential Cell Biology

Quiz 5 To be completed during live session

Live session Group A 10 am Monday September 28

Zoom link https://wakeforest-university.zoom.us/j/93591510877?

MODULE 6 – WEEK OF October 5

Videos 6-1. How cells obtain energy from food

Quiz 6 To be completed before live session

Live session Group A 10 am Monday October 5

Zoom link https://wakeforest-university.zoom.us/j/93591510877?

MODULE 7 – WEEK OF October 19

Videos 7-1. Energy generation in mitochondria

Reading Chapter 14 Essential Cell Biology