BIOL200 Prereading Guide

BIOL 200 Pre-Reading Guide:
Learning Outcomes & Required Readings

(Updated Fall 2020)
Introduction
In this document, you will find two important items: the course and section-specific Learning Outcomes,
and also the Required Readings for each topic. For the Learning Outcomes, you may wish to use this as
a checklist to ensure that you are focusing on the major themes of this course, to better prepare you for
exams.
For the Required Readings, pick either the textbook or the eBook readings (you don’t have to complete
both!). If you are using the (free!) eBook that is available as part of the Canvas course page you will find
that they will cover the same topics as what is outlined here in the textbook readings. For each subtopic,
we provide some questions for you (‘Questions to Consider’) to help you focus your reading, and help
you understand the material.
For easy navigation, there is a Table of Contents provided below on the next page - click on the table to
skip to the section you want.
Overall Course Outcomes

By the end of Biology 200, students will be able to:
1. Demonstrate understanding of the relationship between structure and function, at every level of
cell biology (from individual macromolecules, to the cellular level).
2. Recognize that all aspects of protein function (expression, regulation, modification, transport,
activation, destruction) are ultimately encoded in its sequence, which itself is encoded in the
DNA of the organism.
3. Describe and interpret experimental data based on conceptual knowledge of cell biology.
4. Formulate a scientific argument and defend it using logical reasoning and experimental
evidence.
5. Interpret current primary literature in cell biology, and communicate key findings in writing.
6. Articulate the importance of cell biology within the context of the 'bigger picture' of everyday
life.
BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 1 of 24

Table of Contents
TABLE OF CONTENTS ................................................................................................................................................................... 2

UNIT 1: EUKARYOTIC CELLS & MICROSCOPY............................................................................................................................ 4
TOPIC 1.1: EUKARYOTIC CELLS & ORGANELLES ............................................................................................................................................ 4
Topic 1.1 Learning Outcomes ........................................................................................................................................................ 4
Read Topic 1.1 Online Notes or from Essential Cell Biology ................................................................................................. 4
TOPIC 1.2: MICROSCOPY ............................................................................................................................................................................. 4
Topic 1.2 Learning Outcomes ........................................................................................................................................................ 4
UNIT 2: BIOLOGICAL MEMBRANES ............................................................................................................................................ 5
(OPTIONAL REVIEW) TOPIC 2.0: MACROMOLECULES ................................................................................................................................... 5
................................................................................................................................................................................................................ 5
Topic 2.0 Questions to Consider:................................................................................................................................................... 5
TOPIC 2.1: BIOLOGICAL MEMBRANES .......................................................................................................................................................... 6
Topic 2.1 Learning Objectives ....................................................................................................................................................... 7
TOPIC 2.2 THE LIPID BILAYER......................................................................................................................................................................... 7
TOPIC 2.3: MEMBRANE PROTEINS ................................................................................................................................................................. 8
UNIT 3: NUCLEAR STRUCTURE & FUNCTION ............................................................................................................................... 8
(Optional Review) Topic 3.0 - Nucleic Acids ............................................................................................................................ 9
TOPIC 3.1 NUCLEAR STRUCTURE & PROTEIN IMPORT ..................................................................................................................................... 9
Topic 3.1 Questions to Consider:................................................................................................................................................. 10
TOPIC 3.2 CHROMATIN & CHROMOSOMES ................................................................................................................................................ 10
Topic 3.2 Learning Objectives ..................................................................................................................................................... 10
Read Topic 3.2 Online Notes or from Essential Cell Biology ............................................................................................... 10
TOPIC 3.3: REGULATION OF GENE EXPRESSION .......................................................................................................................................... 11
Topic 3.3. Learning Objectives .................................................................................................................................................... 11
Optional Review Questions for Transcription & Translation ................................................................................................. 12
UNIT 4: ENDOMEMBRANE SYSTEM ........................................................................................................................................... 13
TOPIC 4.1: INTRODUCTION & PROTEIN IMPORT ........................................................................................................................................... 13
TOPIC 4.2: VESICLE TRANSPORT .................................................................................................................................................................. 14
TOPIC 4.3: GOLGI & PROTEIN PROCESSING ............................................................................................................................................... 14
TOPIC 4.4: POST-GOLGI TRAFFIC ............................................................................................................................................................... 15
Topic 4.4 Readings from Essential Cell Biology....................................................................................................................... 15
TOPIC 4.5: ENDOCYTOSIS ........................................................................................................................................................................... 15
UNIT 5: MITOCHONDRIA & CHLOROPLASTS............................................................................................................................ 17
TOPIC 5.1: INTRODUCTION & PROTEIN IMPORT ........................................................................................................................................... 17
TOPIC 5.2 & 5.3 – MITOCHONDRIA & CHLOROPLASTS ............................................................................................................................... 18
Topic 5.2 & 5.3 Learning Objectives ........................................................................................................................................... 18
Read Topics 5.2 & 5.3 Online Notes or from Essential Cell Biology ................................................................................... 18
Topics 5.2 & 5.3 Questions to Consider: .................................................................................................................................... 18
UNIT 6: CYTOSKELETON ............................................................................................................................................................. 19
TOPIC 6.1 OVERVIEW OF CYTOSKELETON; INTERMEDIATE FILAMENTS .......................................................................................................... 19
TOPIC 6.2: MICROTUBULES ......................................................................................................................................................................... 19
TOPIC 6.3: ACTIN FILAMENTS ..................................................................................................................................................................... 20
UNIT 7: CELL CYCLE ................................................................................................................................................................... 22
TOPIC 7.1: CELL CYCLE & CHECKPOINTS ................................................................................................................................................... 22
TOPIC 7.2: CDK-CYCLIN REGULATION ...................................................................................................................................................... 22
TOPIC 7.3: MITOSIS AND CELL DIVISION .................................................................................................................................................... 23
Topic 7.3 Readings from Essential Cell Biology....................................................................................................................... 23

Unit 1: Eukaryotic Cells & Microscopy
The content in this unit should be review from previous courses. ‘Questions to Consider’ are not provided
for this unit, so we encourage you to test out your understanding of the content by looking at the materials
provided at the end of the Unit 1 online notes (‘Unit 1 – External Links, Videos & Interpreting Micrographs’).
Topic 1.1: Eukaryotic Cells & Organelles
Topic 1.1 Learning Outcomes

1. Critically discuss the classical definitions of cells and organelles.
2. Compare and contrast the major characteristics of bacteria and eukaryotes.
Read Topic 1.1 Online Notes or from Essential Cell Biology

The readings for this unit are minimal, so they are not broken down by topic. They are in Chapter 1.
• Unity and Diversity of Cells: pp 1-6 (4th pp 1-5).
• Cells under the Microscope: pp 6-13 (4th pp 5-12), and Panel 1-1
• The Prokaryotic Cell: pp 11-16 (4th pp 12-15)
• The Eukaryotic Cell: pp 16-27 (4th pp 15-26), and Panel 1-2
Topic 1.2: Microscopy
Topic 1.2 Learning Outcomes

1. Distinguish between the four major classes of microscopy: brightfield light microscopy, fluorescence light
microscopy, transmission electron microscopy (TEM), and scanning electron microscopy (SEM).
2. Discuss the major advantages and limitations of each of the four major classes of microscopy.
3. Understand the difference between magnification and resolution, and how each can be used to identify
the type of microscopy used.
4. Recognize the major organelles in light and electron micrographs.
5. Predict the type of microscopy that can be used to detect and study cellular components based on their
size and functional aspect being studied.
6. Interpret the results in micrographs based on scale, magnification, resolution and plane of section.

The readings for this unit are minimal, so they are not broken down by topic. They are all in Chapter 1.
• Unity and Diversity of Cells: pp 1-6 (4th pp 1-5).

• Cells under the Microscope: pp 6-13 (4th pp 5-12), and Panel 1-1
• The Prokaryotic Cell: pp 11-16 (4th pp 12-15)
• The Eukaryotic Cell: pp 16-27 (4th pp 15-26), and Panel 1-2

Unit 2: Biological Membranes
Use the Pre-reading Guide below to direct how you focus your reading of these sections, and give yourself
a first introduction to the material that we will practice, apply, and solidify in class. While reading, focus
on the particular aspects discussed here, and try to answer the given questions. Then do the pre-reading
quiz on Canvas. NOTE: This reading is quite long, due to the optional background material. Plan
accordingly.
Much of this unit requires a solid foundation from previous courses in biology. If you find yourself having
difficulty with any of this material, (e.g. if you used a class other than UBC’s BIOL112 as your biology pre-
requisite, or it has been a long time since you took it, and need more review), see the additional
recommended textbook reading listed on each topic on Canvas (especially Topic 2.1).
(Optional Review) Topic 2.0: Macromolecules
You are fully responsible for this topic as self-study; it will not likely be covered in class in detail. Since this
material is considered to be review, you may not need to read all sections. We suggest reading this guide
to see how confident you are with the material before you spend too much time on this part of the
readings. We will revisit these topics throughout the term, so make sure you are solid in your understanding
of the basics.
Review of Underlying Chemistry

• Chemistry of Water as a Solvent – Chapter 2: Panel 2-2, pp 68-69 (both editions)
• The Use of Energy by Cells – Chapter 3: pp 82-88 (4th ed. pp 83-90)
• Free Energy and Catalysis – Chapter 3: pp 88-100, Panel 3-1 pp 94-95 (4th ed. pp 90–103, Panel 3-1 pp 96-97)
• Activated Carriers and Biosynthesis – Chapter 3: pp 101-112, skip pp 102-103 (4th pp 103-116, skip pp 104-
106).
Biological Macromolecules & Chemical Bonds:

• Chemical Bonding – Chapter 2: pp 40-50 (both editions), Panel 2-1 pp 66-67 (both editions).
o Non-Covalent bonding – pp 46-50 (4th pp 47-50), Panel 2-7 pp 78-79 (both editions).
• Biological Macromolecules – Chapter 2: pp 50-64 (4th pp 50-79).
o Lipids – pp 54 and 55 (both editions), Panel 2-5 pp 74-75 (4th Panel 2-4 pp 72-73)
o Amino Acids – pp 56 (4th pp 55-56), Panel 2-6 pp 76-77 (4th ed. Panel 2-5 pp 74-75)
o Nucleic Acids – pp 56-58 (4th pp 56-57), Panel 2-7 pp 78-79 (4th ed. Panel 2-6 pp 76-77).
o Structure of DNA – Chapter 5: pp 174-176 (4th pp 172-173 &177-179).
Transcription & Translation:

• Transcription – Chapter 7: pp 228-237(4th pp 224-232)
• Translation – Chapter 7: pp. 243-259 (4th pp 238-253)
Topic 2.0 Questions to Consider:

Chemical Bonds & Non-Covalent Interaction
• What are the different types of non-covalent bonds that are possible? Be able to understand and translate
between both the chemical terms (e.g. dipole-dipole, etc.) and the common names (e.g. van der Waals)
for these bonds/ interactions.
• What is the difference between a hydrogen bond versus an N-H (or O-H) bond?
(continued next page)

• Cell biologists often use the term “hydrophobic interactions” to describe what happens when nonpolar
molecules are in an aqueous solution. Why is this not a completely accurate term, even though it is a
useful shorthand?
Properties of Biological Macromolecules

• What is the monomer of a protein? Of a nucleic acid? Of a carbohydrate?
• For polymeric macromolecules, what does “polarity” mean? How is this meaning different than the
meaning of polarity of chemical bonds? Are there other ways that this term could be interpreted that
should be considered?
• When considering polymers, how are lipids different than other macromolecules?
• What type of reaction typically brings monomers together?
• What is meant by ‘extensibility’? What is an ‘activated carrier’? What is meant by ‘denaturation’?
Lipids
• What are the structural differences and similarities between phospholipids, sterols, and fatty acids?
• Given their structural diversity, why are lipids considered all in the same category? How does this
categorization of lipids differ from the way we categorize other macromolecules?
Proteins
• The primary structure of a protein consists of the sequence of amino acid residues.
• What is an “amino acid residue”?
• What type(s) of bonds stabilize the primary structure?
• Why is the order of amino acids in a protein important?
Secondary structures are stabilized by intra-chain hydrogen bonds occurring over relatively short distances.
• What type(s) of bonds stabilize the secondary structure?
• Which parts of the amino acids are involved in these non-covalent interactions that form the secondary
structure? (R-group and/or backbone?)
Tertiary structure is stabilized primarily by hydrogen bonding between more distantly separated residues within a
peptide chain and by hydrophobic interactions of non-polar amino acid residues.
• What type(s) of bonds stabilize tertiary structure? What is meant by a ‘domain’?
• Which parts of the amino acids are involved in these non-covalent interactions that form the tertiary
structure? (R-group and/or backbone?)
• What types of amino acids are usually found in the center of a soluble protein? Why does this help to
stabilize the protein?
• How can chaperone proteins facilitate protein folding in two different ways? You can refer to Figures 4-8 &
4-9 (4th ed. Figures 4-9 & 4-10) which can be found under ‘Canvas > Additional Resources > Review
Materials > Review – Amino Acids & Proteins’, towards the bottom of the page).
Quaternary structure is the interaction of multiple polypeptide chains to form a protein composed of multiple
subunits.
• What type(s) of bonds stabilize quaternary structure?
• Which parts of the amino acids are involved in these non-covalent interactions that form the quaternary
structure? (R-group and/or backbone?

Topic 2.1: Biological Membranes
Topic 2.1 Learning Objectives

1. Discuss the structural and functional features of biological membranes and relate how the different
macromolecular components (lipids, proteins & carbohydrates) interact to form biological membranes.
2. Describe the chemical properties of phospholipids, cholesterol, and glycolipids, and know how these
properties contribute to the lipid bilayer structure and function.
3. Recognize the 20 amino acids according to their chemical properties, and their 3-letter and 1-letter
abbreviations.
4. Differentiate between the primary, secondary, tertiary and quaternary levels of protein structure.
5. List and discuss the role of non-covalent bonds in protein folding and stabilization of protein structure.
6. Illustrate how the primary sequence and the environment of a protein influence its final 3D structure.

Protein Folding Review – Chapter 4:
o Protein structure: pp 117-136 (4th ed. pp 121-143)
o Antibodies in science: pp 138-139 (4th ed. pp 143-144) and Panel 4-2, pp 147-148 (both editions)
• Membrane Lipid Review – Chapter 11: pp 367-370 (4th ed. pp 361-364)

1. The membrane is a bilayer, made up of both lipids & Proteins
• What sort of configuration would be likely with a mixture of phospholipids and water? How would this
compare with a mixture of triglycerides and water?
• Could you have a membrane bilayer in a non-aqueous medium? Why or why not? Explain in terms of the
stability of the system.
• How might the combination of proteins and lipids in the membrane affect membrane structure and/or
function?
2. The Membrane is Selectively Permeable
• Why is selective permeability such an important property for the cell?
• Would you expect the permeability of biological membranes to water to be higher or lower than that of a
phospholipid bimolecular leaflet? Why or why not?
3. The Membrane is organized but Fluid & 4. The Membrane is Asymmetric
• What do we mean when we say that the membrane is a 2-dimensional fluid?
• How can the 2 leaflets of the membrane be different? How might that contribute to membrane structure
and/or function?
Topic 2.2 The Lipid Bilayer

1. Describe factors affecting or regulating the fluidity of lipid bilayer.
2. Predict the relative fluidity of membrane bilayers based on their lipid composition.
3. Explain how Fluorescence Recovery After Photobleaching (FRAP) works, and interpret results of FRAP
experiments.
4. Describe membrane asymmetry and explain the origin of the asymmetric distribution of membrane lipids.

Chapter 11: pp 365-374 (4th ed. pp 360-369, includes lipid review pages listed in Topic 2.0

• Why is membrane fluidity an important property, from the perspective of the cell?
• How does the cell modulate fluidity of its membranes, and under what kinds of conditions might it need to
do so? Are these conditions equally present in all cells of all different species? Why or why not?
• What is the purpose of using FRAP to examine membranes?
Topic 2.3: Membrane Proteins

1. Distinguish between integral and peripheral proteins with regard to their solubility properties, structure and
manner of attachment to membranes.
2. Describe the techniques used to study membrane proteins:
a. Bioinformatics approach to predict transmembrane domains in proteins – e.g. hydropathy plots
b. Biochemical approaches to determine membrane protein type, components and orientation –
e.g. SDS-PAGE, fluorescence staining, carbohydrate staining for glycoproteins.
3. Interpret results from SDS-PAGE, fluorescence and glycoprotein staining experiments to determine
orientation and location of proteins and glycoproteins in a membrane.
4. Predict the hydropathy profile for a given protein given its primary amino acid sequence, or for a given
hydropathy plot, predict the amino acid composition of the protein domains within a membrane protein.

• Chapter 11: pp 375-end of chapter (4th ed. pp 369 - end of chapter)

Integral and peripheral membrane proteins
• What are some examples of amino acids that are likely to be on the surface of an integral membrane
protein? What types of amino acids will be on the surface of a peripheral membrane protein?
• What sort of amino acids would you expect to occur in transmembrane domain of a protein immediately
adjacent to the hydrophobic residues? Why? How would they interact with the membrane?
• Why are transmembrane proteins insoluble when they are removed from the membrane?
Determining protein location & orientation experimentally

• What are the 2 experimental approaches that are described in this section? What is the main purpose of
each? In what situation would you choose one approach or the other?
The Plasma Membrane

• Look at Figure 11-20 (4th ed. Figure 11-19) from your textbook. What kinds of plasma membrane proteins
are present? Can you relate the structure of these proteins to their respective functions? Can you predict
the different types of amino acids that may be present at their active sites?
• Fibronectin is a large glycoprotein present in the extracellular matrix (ECM). If a cell contains a mutation
that leads to a loss of fibronectin, how would plasma membrane attachment to the cytoskeleton, and the
extracellular matrix, be affected?
• What is the difference between the types of macromolecules found on the inner side of the membrane,
and the outer side?
• What types of macromolecules are found in the extracellular matrix?

Unit 3: Nuclear Structure & Function
Use the Pre-reading guide below to direct how you focus your reading of these sections, and give yourself
on the particular aspects discussed here, and try to answer the given questions. Then do the quiz on
Canvas.
Note: Completion of this Unit Pre-Reading will require a solid understanding of the structure of DNA &
Nucleotides.
(Optional Review) Topic 3.0 - Nucleic Acids

Because this is review from First Year Biology, you are largely responsible for this topic as self-study; it will
not likely be covered in class. You may or may not need to read these review pages. If you find yourself
having difficulty, please seek help from your peers, TAs, or instructor, or review your notes from your first-
year biology courses.
You may need to review your first-year notes, or the review page posted on Canvas (under Additional
Resources > Review Material > Review – Nucleic Acids).

Nucleic Acids – Components
• Considering the sizes, and the names, of the bases: which bases are purines, and which are pyrimidines?
• What is the name of the covalent chemical linkage in nucleic acids?
• What is the directionality (polarity) of a nucleic acid strand? During nucleic acid synthesis, new
nucleotides are added to which end?
Nucleic Acids as ‘Informational Polymers’

• What is meant by ‘informational’ here?
• What are the chemical differences between DNA and RNA?
• What non-covalent interactions (bonds) stabilize nucleic acid 3-D structure?
• Where else have you seen the hydrophobic effect as a driver of macromolecular assembly?
Topic 3.1 Nuclear Structure & Protein Import

1. Describe the structure of an interphase nucleus, and recognize structural elements in different kinds of
microscopy.
2. Describe the nuclear pore complex (NPC) and explain the different types of nuclear transport
mechanisms.
3. Explain how proteins are transported into and out of the nucleus, including the roles of the Nuclear
Localization Signal (NLS), nuclear transport receptors, and the NPC itself.
4. Analyze experimental evidence from fluorescence microscopy and explain how it provides evidence that
the primary sequence of a protein contains all of the necessary information to determine whether a
protein is imported into the nucleus.

• The Interphase Nucleus – Chapter 5: pp 182-183 + 189-192 (4th ed. pp 183-184 + 190-191)
• Nuclear Import – Chapter 15: pp 496-505 (4th ed. pp 488-497)

The Nuclear Envelope
• What is meant by a 'double membrane'? How is this different than the plasma membrane? Draw a diagram
of the lipid arrangement in the nuclear envelope, and the lipid arrangement in the plasma membrane.
• How is the structural integrity of the nucleus maintained? How does this also facilitate the breakdown and
reformation of the nucleus during mitosis?
The Nucleolus & Nuclear Pores

• What are the macromolecular components of the nucleolus organizer regions?
• What kinds of molecules require transport into/ out of the nucleus?
• What is the major factor that determines whether a molecule requires active or passive transport through
the nuclear pore?
Protein Targeting to the Nucleus

• Why do proteins require a targeting signal to enter the nucleus? When do proteins acquire the targeting
signal?
• What is the difference between something being necessary for a process versus something being sufficient
for a process?
• Why do you think it is important that the NLS remains part of the protein after it has entered the nucleus?
• Is export from the nucleus controlled in the same way that import is? In what ways is it different?
Topic 3.2 Chromatin & Chromosomes

1. Discuss how proteins and DNA interact to form chromosomes, starting with the 2nm naked DNA molecule
to the structure of interphase chromatin, including euchromatin, heterochromatin, and chromosomal
loops.
2. Explain how the primary, secondary, tertiary and quaternary levels of histone structure contribute to
nucleosome assembly.
3. Interpret experimental results providing quantitative information about the spacing of nucleosomes and
the amount of DNA associated with these structures.

• Chromosomes – Chapter 5: pp 178-183 (4th ed. pp 179-183)
• Chromatin packing: pp 183-187 (4th ed. pp 184-187)

Chromatin is formed from DNA & Histones
• What is the difference between histone & non-histone proteins?
• Explain why this statement is True or False: Scientists refer to histones as “basic” because they are
fundamentally important proteins.
• The core histones (H2A, H2B, H3 & H4) all have a common general structure. Describe the regions of the
general structure shown. What role might these regions have in histone protein structure & chromatin
assembly?
• What is the purpose of the core histone tails?
• How does histone H1 fit into the packaging of DNA?
• How does the 11nm fibre form (i.e. the ‘beads on a string’ model)? How is it different from the 30nm fibre?
• What is the level of packaging of DNA in the interphase nucleus?

Experimental Evidence for Nucleosomes in Eukaryotes: Nuclease Digestion
• How does the gel electrophoresis here differ from the gel electrophoresis used to separate membrane
proteins in Unit 2?
• See Figure 5-20. What is meant by ‘linker DNA’? What type of molecule is a ‘nuclease’? What is its
substrate? Why and how are nucleases useful in determining chromatin structure and nucleosome size?
• How does micrococcal nuclease work? Why does the time length of the exposure of the chromatin to the
micrococcal nuclease change the results of the experiment?
Topic 3.3: Regulation of Gene Expression
Topic 3.3. Learning Objectives

1. Discuss the different types of DNA and histone modifications and their roles in the regulation of gene
expression.
2. Distinguish between the different types of transcription factors (e.g. basal, activators and repressors) and
explain how their interaction with specific regulatory regions of DNA regulate transcription.
3. Discuss how mRNA processing events (e.g. cap, tail) can regulate overall gene expression.
4. Discuss the mechanism and specificity of mRNA splicing events and explain how alternate splicing
increases the diversity of protein products encoded from a single gene.
5. Illustrate the importance and specificity of macromolecular interactions involved in regulation of gene
expression by interpreting experimental evidence in eukaryotes.

• Transcript Processing – Chapter 7: pp 237-243 (4th ed. pp 232-238)
• Regulation of Gene Expression
o Chapter 8: pp 267-275 (4th ed. pp 261-266) + pp 276-282 (4th ed. pp 270-277)
o Note that the pages describing ‘How We Know - The Story of Eve’ are not required reading.

Control of Gene Expression: Control of Chromatin Structure
• Terminology check: what is the difference between heterochromatin and euchromatin? What is the
difference between constitutive and facultative heterochromatin? Figure 5-31 may help here.
• How are the histone tails used to influence chromatin structure?
• Consider Figure 5-27. What do the yellow circles represent? How do histone modifications cause the
transition from the top structure in the figure, to the bottom? Which chromatin structure in the figure (the
top one or the bottom one) is likely to have more genes being transcribed from it?
Control of Gene Expression: Transcription Factors

• Review the general features of a transcription unit. What are the differences between the prokaryotic
transcription unit you saw in BIOL112 and the eukaryotic one described here?
• What kinds of transcription factors exist and how do they influence transcription?
• How do histone-modifying enzymes work, and how do they promote/ inhibit transcription?
Control of Gene Expression: Post-transcriptional Processing of mRNA

• Where does RNA processing take place?
• RNA processing is an “expensive” process for the cell. Given the cost, what are some benefits to the cell?
• Where is the information for the “instructions” for processing any particular transcript?
• What are the primary roles of each of the three major mRNA processing steps?
• What are the stages in mRNA splicing? What machinery is required?
• Consider the 3rd edition Figure 7-21 (‘Example of alternative splicing – Tropomyosin’). How can different
cells synthesize different mature mRNA from the same gene?

Optional Review Questions for Transcription & Translation
Because this is review from First Year Biology, you are largely responsible for this topic as self-study; it will
not likely be covered in class. You may or may not need to read these review pages. If you find yourself
having difficulty, please seek help from your peers, TAs, or instructor.
Topic 2.0 online has links for reviews on the processes of Translation & Transcription, which may helpful.
Optional Readings from ECB- Transcription & Translation:

• Transcription – Chapter 7: pp 228-237(4th pp 224-232)
• Translation – Chapter 7: pp. 243-259 (4th pp 238-253)
Questions to Consider:
1. Process of Transcription
The Hereditary System in Eukaryotes
• What are the two major roles of DNA?
• What two processes take the information in the genome to synthesize a functional product in the cell?
• Throughout this reading, notice any differences between prokaryote and eukaryote transcription .
Transcription
• Familiarize yourself with the terminology used to describe the structure of a transcription unit. For practice,
try drawing a transcription unit and labeling it without looking at the notes.
Initiation, Elongation & Termination

• What types of molecules are parts of the transcription initiation complex?
• Where does the transcription initiation complex bind the DNA? Where is this site relative to the
transcription start site? In what order is this complex assembled?
• Why are there such a large variety of transcription regulators? How might this variety help the cell respond
to its environment?
• What direction does the transcription complex move on the DNA? How does the transcription complex
recognize which orientation to bind the DNA?
2. Process of Translation
General Features of the Genetic Code
• The genetic code is universal. What does this imply in terms of evolution?
• Considering the genetic code, describe the difference between the terms “redundant” and “ambiguous”.
• If the sequence can be read at any starting point, why are there only three reading frames (instead of
nearly-infinite)?
• What machinery is involved in tRNA activation? Why are tRNA molecules considered the ‘translators’ of
the genetic code?
• Given that there is only one start codon, how is it possible that mRNA can be simultaneously producing
several copies?
Translation
• What are the components of the translation initiation complex?
• Practice the steps of translation elongation: can you narrate all of the steps required in elongation to a
classmate?
• What are the steps involved in translation termination?

Unit 4: Endomembrane System
quiz on Canvas.
NOTE: This reading is quite long. Plan accordingly. If you did not do the Translation Review in the last pre-
reading, you may want to review it prior to Topic 4.1.
Topic 4.1: Introduction & Protein Import

1. Explain the structural & functional relationships between the different compartments of the
endomembrane system, and identify them on micrographs.
2. Describe how proteins are targeted and imported into the endoplasmic reticulum and compare these
mechanisms to protein targeting and import into the nucleus.
3. Predict the signal sequences required to insert a protein into the ER membrane in any orientation, and
predict protein topology from a corresponding domain map.
4. Discuss the role of chaperones in protein folding and role of proteasomes in quality control of misfolded
proteins in the secretory pathway.
5. Describe and interpret the results of the different experimental tools studying the secretory pathway.

This unit covers almost all of Chapter 15:
• Overview of membrane-bound organelles
o Chapter 15: pp 496-498 (4th ed. pp 487-490). This overlaps with Topic 3.1 Readings
o The ER as part of the secretory pathway – Chapter 15: pp 515-518 (4th ed. pp 507-510)
o ‘How We Know’: pp 512-513 (both editions)
• Protein import into the ER – Chapter 15: pp 507-511 (4th ed. pp 498-502)

Protein Processing & the Endomembrane System
• What are the benefits to the cell of protein processing?
• Look at the second figure in this subtopic (from Wikipedia). Try writing a figure legend/caption to describe
it.
• When we say a protein is “tagged for destruction” with ubiquitin, what does this mean? Describe the
subsequent processes, considering Figure 7-44.
Processing of Endomembrane Proteins & Structure of the ER

• What is the major difference between the rough and smooth ER? When we discuss protein targeting to the
ER, which type of ER are we discussing?
• There are 3 main types of proteins that enter the endomembrane system… what are they? What kinds of
structural differences are there between these 3 types? What about functional differences?
• Consider the mis-folded protein response (Figure 15-25). This is an energetically expensive process for the
cell! Why do you think the cell spends so much effort and resources to make sure proteins are folded
properly?
(continued on next page)

Import of Proteins into the Endomembrane System is Co-Translational
• Look at Figure 15-14, and describe the steps of protein targeting to the ER that are shown in the figure.
• Look at Figures 15-15, 15-16, and 15-17. Compare the insertion of soluble, single-pass membrane, and
double-pass membrane proteins. What are the similarities and differences? In each case, how does the
cell determine the targeted location of the protein? Describe and name the signals, and describe the
way in which the cell machinery recognizes each signal. (It might help you to make a table to organize
your knowledge here: use the types of proteins as rows, and the questions listed above as columns.)
• In the figure under “Domain Mapping of Proteins” – try to answer the two questions shown.
• In the figure under “A Final note on ‘Sidedness’” – what is the major take-home message of the figure?
Can you write a figure caption?
Experimental Methods for Studying the Endomembrane System

• You can skip this topic for the pre-reading and quiz, though this subject is still an essential and required part
of Unit 4’s material. This topic will be introduced in class, using the online notes as a reference.
Topic 4.2: Vesicle Transport

1. List the 4 stages of vesicle transport, and list the proteins machinery involved at each step.
2. Explain how vesicle coats facilitate cargo loading and vesicle budding.
3. Discuss the importance of maintaining specificity in z both docking and fusion of vesicles at their target
compartments, and how Rabs, tethers and SNAREs facilitate this process.
4. Discuss and illustrate how the orientation of membrane proteins in the lipid bilayer is maintained during
transport and after fusion of vesicles with target membranes.

This unit covers almost all of Chapter 15
• Chapter 15: pp 511-515 (4th ed. pp 503-507)

Vesicle Transport
• What are vesicles? How are they formed? What do they carry? What is their role in the cell?
• Consider the text, and Figure 15-21. What are the general components of vesicle coats? What are the
roles of these components?
• What process determines the contents of a given vesicle?
• How do vesicles move through the cell? How do they deliver their contents at their destination?
• Terminology check: what are COPs, clathrin, cisternae, and SNAREs?
Topic 4.3: Golgi & Protein Processing

1. Discuss the functional compartmentalization of the Golgi structure, and recognize the Golgi apparatus
using different types of microscopy.
2. Describe the sequence of events occurring duringz protein glycosylation in the ER and Golgi.
3. Use experimental evidence to determine how membrane and cargo are transported through the Golgi
apparatus.

This unit covers almost all of Chapter 15

Golgi & Protein Processing
• Using the notes, list the path a protein takes from initial translation to its eventual location in the Golgi. How
is this protein recognized and processed along the way, to ensure that it reaches the Golgi?
• Terminology check: in cell biology, what is meant by the terms cis and trans? (The animation may help)
• To understand the two major models of how cargo moves through the Golgi, try to draw diagrams of the
Vesicle Transport Model, and the Cisternal Maturation Model. What other models can you envision?
• What are the names of the major regions of the Golgi? What direction do trafficked proteins move
through the Golgi? Why do we call the trans Golgi Network (TGN) a ‘protein sorting centre’?
• What does the term “protein processing” mean? What are some forms of post-translational modification?
Which ones did we see already in the ER? What is/are the most important type(s) of protein post-
translational modification that takes place in the Golgi?
Topic 4.4: Post-Golgi Traffic

1. Describe the secretory, lysosomal, and endocytic pathways and list all of the components of these
pathways.
2. Compare and contrast constitutive and regulated secretion and explain the importance of each.
3. Discuss the structure and function of lysosomes, and explain how they mature from late endosomes.
4. Trace the path of a newly synthesized lysosomal protein to its final destination, and compare this to the
path of proteins to all the other destinations within the endomembrane path.
Topic 4.4 Readings from Essential Cell Biology

This unit covers almost all of Chapter 15.
• Secretion: pp 519-523 (4th ed. pp 511-515). Includes ‘How We Know’ from Topic 4.1
• Lysosomal Pathway: pp 527-528 (4th ed. pp 519-520)

Secretory pathway (aka Exocytosis)
• Terminology check: What does ‘secretory’ mean? What does the term ‘constitutive’ mean?
• Why do we call the trans Golgi Network (TGN) a ‘protein sorting centre’?
• Why might the cell need two types (regulated and constitutive) of secretory pathways? What types of
molecules would you expect to be transported by one or the other?
• What is meant by an “aggregate” that is formed by proteins in the TGN?
• How might different proteins be affected by acidic and neutral conditions? What might this tell you about
what features of proteins are important in determining the final destination of the protein (i.e., regulated
vs. constitutive secretory pathway)?
The Lysosomal Pathway

• What is the role of the lysosome in the cell?
• What types of proteins are transported to lysosomes from the Golgi? Why do you think they are sent there?
• What is meant by ‘recycling’ of mannose-6-phosphate receptors?
Topic 4.5: Endocytosis

1. Discuss the structure and function of endosomes, and differentiate between early and late endosomes.
2. Compare and contrast between constitutive and receptor-mediate endocytosis.
3. Trace a molecule from the exterior of the cell to the lysosome along the endocytic pathway.
4. Explain with examples how receptor proteins facilitate endocytosis.
5. Compare and contrast receptor recycling in the lysosomal and endocytic pathways.

This unit covers almost all of Chapter 15.
• Chapter 15: pp. 523-527 (4th ed. pp 515-519)

Endocytosis
• Compare the three different types of endocytosis in terms of these components: the signal, the machinery,
and the cargo. For these components, what are the similarities and differences?
• Terminology check: what is the difference between endosomes, lysosomes, vacuoles, and vesicles?
• What is the role of the endosome?
• What can happen to a receptor when it arrives at the endosome? What locations can the endosome’s
cargo be taken to?
• What type of molecule is mannose-6-phosphate? What is the role of this molecule in the endosome?
• What types of material are sent to the lysosome from the cell surface? Why do proteins from both the Golgi
and the cell surface end up in the lysosome together?

Unit 5: Mitochondria & Chloroplasts
quiz on Canvas.
Topic 5.1: Introduction & Protein Import

1. Explain the unique characteristics of mitochondria and chloroplasts that are the result of their evolutionary
origin as bacterial endosymbionts.
2. Describe (or discuss) the post-translational targeting of proteins to mitochondria and chloroplast,
depending on specific domains in its primary sequence and its final destination within these organelles.
3. Compare and contrast protein targeting to mitochondria and chloroplasts with targeting to other
organelles/destinations already described.

• The Endosymbiont Theory (will not be covered in class, but you are expected to understand this theory
based on prior knowledge or readings below)
o Chapter 1: Figures 1-19, 1-20 & 1-29 (4th ed. Figure 1-18, 1-20 and 1-28). Also, pp 24-27 (4th ed. pp 23-
26). Panel 1-2 not required, but useful.
o Chapter 14: pp 488-490 (4th ed. 479-481). Last section on Methanococcus is not required in this
reading.
• Protein Targeting to the Mitochondria and Chloroplasts – Chapter 15: pp 505-506 (4th ed. pp 497-498)

Mitochondria & Chloroplasts Evolved from Free-Living Bacteria
• Familiarize yourself with the structural features of bacteria and compare/relate them to the structure of
mitochondria and chloroplasts.
• Compare the relative permeability of the outer and inner membranes in bacteria, mitochondria and
chloroplasts. Why is it important that the internal membranes be selectively permeable? What types of
transporters would you predict to be in the inner membrane?
• Analyze the table comparing properties of the genomes and protein synthesizing machinery. How do
mitochondria/ chloroplasts compare to eukaryotic cells, to bacterial cells?
• Look at the phylogenetic tree for cytochrome C. What is the significance of the red and green clusters?
• Why are the genomes of mitochondria and chloroplasts smaller than free-living bacteria?
Protein Import into Mitochondria & Chloroplasts

• What are the steps to protein import into the mitochondria (shown in Figure 15-11b)? How are they
different from what’s required for import into the chloroplast?
• Compare protein import into mitochondria/chloroplasts to other organelles such as the nucleus and the
ER. What are the unifying features? What are the differences?
• Can you think of the consequence of cleaving the import signal after the protein has been imported into
the organelle? Why are some signals retained in other organellar transport mechanisms?

Topic 5.2 & 5.3 – Mitochondria & Chloroplasts
Topic 5.2 & 5.3 Learning Objectives

Topic 5.2 – Mitochondria
1. Explain and interpret micrographs of mitochondria in cells.
2. Relate mitochondrial structure to the chemiosmotic coupling of proton pumping and ATP formation in
mitochondria during the process of oxidative phosphorylation.
Topic 5.3 - Chloroplasts
1. Recognize chloroplasts and its various compartments on electron micrographs.
2. Discuss the chloroplast structure and its relevance to the process of photophosphorylation and
photosynthesis.
3. Compare and contrast, chemiosmotic coupling of proton pumping and ATP formation in mitochondria
and chloroplasts.
4. Explain the relationship between mitochondria and chloroplasts in plant cells.
Read Topics 5.2 & 5.3 Online Notes or from Essential Cell Biology
Topic 5.2 - Mitochondria
• Chemiosmotic coupling of ATP synthesis – Chapter 14: pp 456-458 (4th ed. pp 448-450)
• Mitochondria – Chapter 14: pp 459-461 (4th ed. pp 451-461)
• Refresher on the chemistry behind electron transport & proton pumping: Chapter 14 pp 461-469 (both ed.)
Topic 5.3 - Chloroplasts
• Chloroplasts – Chapter 14: pp 469-top of 479 (both editions)
Topics 5.2 & 5.3 Questions to Consider:

Generation of ATP
• Compare and contrast ATP generation in the mitochondria and chloroplast. Are the mechanisms the
same? How?
• What is the ultimate goal of each organelle? What are they trying to synthesize for the cell? How might the
production of ATP in each case support that goal?
• Examine the Flash animations of chemiosmotic generation of ATP in bacteria (with/ without thylakoids).
How does the direction of proton flow in the bacterial cells compare with what’s happening in the
mitochondria and chloroplasts (you can compare with Figure 14-49)?
Mitochondrial Structure & Function

• Familiarize yourself with the structural features of mitochondria & how they relate to the structure of
bacteria.
• What is the overall function of mitochondria? Review the inputs and outputs of the major metabolic
reactions that occur in the mitochondria (based on BIOL112 or equivalent material).
• Try and place the major reactions that occur in the mitochondria in the proper compartment. Where are
the electron transport chain (ETC) and the ATP synthase located? Where does the Citric Acid Cycle take
place? What about glycolysis, which feeds into the mitochondrial process?
Chloroplast Structure & Function

• Compare chloroplast structure to mitochondria structure; think about how they relate to each other in
structure and metabolic function.
• Familiarize yourself with the inputs and outputs of photosynthesis. What is the purpose of photosynthesis?
• Think about where the stages of photosynthesis take place in relation to chloroplast structure. Where is the
ETC located? Where do the ‘dark reactions’ (aka the carbon fixation cycle) take place?
• What is the purpose of ATP production in the chloroplast compared to the mitochondria?
• How do the light-dependent and light-independent reactions of photosystem relate to each other?
How do these two Organelles Work Together?

• Explore the relationship between mitochondria and chloroplasts. Why do they rely on each other?
• Think about the inputs of aerobic respiration that occurs in the mitochondria. Where did they come from?
• Now think about the outputs of aerobic respiration. Where do they go?
• Why might plants need BOTH mitochondria and chloroplasts?

Unit 6: Cytoskeleton
quiz on Canvas.
In this unit, focus on understanding the structures and the functions of the different types of cytoskeletal
elements. What are the structural and functional similarities and differences in the molecules involved?
Topic 6.1 Overview of Cytoskeleton; Intermediate Filaments

1. Compare and contrast the structure and function of the three types of cytoskeletal elements: actin
filaments, intermediate filaments and microtubules.
2. Identify the different types of cytoskeletal elements on different type of micrographs.
3. Discuss different types of intermediate filaments, and correlate their structure with the strength of the
assembled, functional cytoskeletal element.

This Unit covers most of Chapter 17

Overview of Cytoskeleton; Intermediate Filaments
• The cytoskeleton is involved in giving the cell its shape and resisting mechanical forces. Give some
examples of what kinds of forces these might be, acting on different types of cells in the body.
• What are the three types of elements in the cytoskeleton? What are the roles of each?
• What are the three types of fibers in the cytoskeleton? What are the roles of each?
• Consider Figure 17-4, showing intermediate filament assembly. Describe in words the structure of
intermediate filaments. How are intermediate filaments assembled? What types of interactions hold
together these assemblies?
• What are two major roles of intermediate filaments?
Topic 6.2: Microtubules

1. Compare in vivo (in cells) and in vitro (in test tubes) microtubule polymerization.
2. Interpret in vitro microtubule polymerization curves in terms of microtubule dynamics.
3. Explain the process of dynamic instability, focusing on how tubulin dimers (alpha/ beta) interact non-
covalently to make microtubules with a ‘plus’ and ‘minus’ end.
4. Interpret live-cell images of microtubules undergoing dynamic instability and explain the current model of
how GTP binding to tubulin can bring about this dynamic behaviour.
5. Explain how motor proteins work and how their movement relates to the polarity of the microtubule.
6. Provide examples of how proteins can interact with microtubules or tubulin to influence their structure,
which, in turn, will influence function.

• Chapter 17: pp 580-590 (4th ed. pp 571-579). The section on ‘How We Know’ is not required reading.

Introduction
• Consider Figure 17-12, showing the structure of microtubules. Describe in words the structures shown in the
image. How are microtubules assembled? What types of interactions hold these proteins assemblies
together?
• What is meant by “polarity” of a microtubule? How is it different from other instances when you’ve
encountered this term?
• What is the structure and role of a Microtubule Organizing Centre (MTOC)?
Microtubules & Dynamic Instability, Stabilizing MTs

• Consider Figure 17-15. Describe in words the molecular difference between the process of growing
microtubules, and the process of shrinking microtubules. Which end of the microtubule do these images
represent?
• What does the term “dynamic equilibrium” mean?
• What does the term “critical concentration” mean?
• What is meant by “selective stabilization” of microtubules? How is this stabilization achieved?
Microtubule Function: Motor Proteins

• Consider Figure 17-17. What might be some examples of “particles” in the cell that are being moved
along the microtubule?
• What two motor proteins are involved in transport along microtubules? What are their similarities and
differences, in terms of structures and functions?
• From a molecular perspective, how does the polarity of the microtubule determine the direction of
transport?
• What is/are the role(s) of cilia and flagella in cell biology?
Topic 6.3: Actin Filaments

1. Describe in vitro actin filament structure and polymerization, and the role of monomer concentration and
ATP in dynamic instability.
2. Correlate in vivo actin filament polymerization and organization at the cell cortex with its function of
deforming the plasma membrane and regulating cell shape.
3. Relate how actin binding proteins influence actin filament polymerization and organization to regulate
microfilament function (e.g. cell motility).
4. Interpret results from experiments using drugs that disrupt actin filaments and compare with equivalent
experiments that disrupt microtubules.
5. Explain the function of myosin motors, and their role in contractile bundles as well as in other cellular
contexts such as cytoplasmic streaming.

• Section on muscle contraction is optional (pp 600-end of chapter, 4th ed. pp 592-end of chapter). We will
not be going into depth about this function, but students who wish to pursue certain career futures may be
interested.

Actin Filaments
• Consider Figure 17-31a, noticing the cycle of ATP/ADP exchange. Where have we seen a similar process
before?
• What the terminology that is used to describe the polarity of actin filaments?

• Consider Figure 17-32. For each of the types of cross-linked arrays, where in the cell is each array
functional?
• What is the structure of myosin I and myosin II? What are their functions in the cell?
• What direction does myosin move, along actin filaments?
• How does myosin activity compare with other motor proteins we have discussed? What are the similarities
and differences?
Drugs that influence Actin & Microtubules

• Note that you do NOT need to memorize the drugs in Tables 17-1 & 17-2. Instead we suggest that you
return to this table after we finish Unit 6, and considering the thought questions below it. This would be a
good study option to help bring together your understanding of cytoskeletal functions.

Unit 7: Cell Cycle
quiz on Canvas.
Topic 7.1: Cell Cycle & Checkpoints

1. Review the overall organization of the cell cycle and its relation to cell division (mitosis and cytokinesis).
2. Use experimental evidence to distinguish what phase of the cell cycle that a cell is in (i.e. G1, S, G2 or M-
phase).
3. Explain the concept of checkpoint control of cell cycle and give examples of what types of conditions
should be met before S and M phases proceed.


Cell Cycle & Checkpoints
• What is meant by a “cell cycle checkpoint”? Why are checkpoints important? Why do different
checkpoints have different criteria (conditions that must be met) to proceed?
• What are the different properties of the cell during different phases (M, S, G1/G2)?
• Look at the animations for asynchronous and synchronous cell populations. What is the main difference
between these populations?
• In the animations, why is “D” labelled as “1.0/0.0”?
Topic 7.2: CDK-Cyclin Regulation

1. Describe how specific protein modifications (e.g. phosphorylation and ubiquitination) result in
activation/deactivation of cyclin-CDK complexes to regulate cell cycle checkpoints.
2. Explain how the activation of the cyclin-CDK complexes results in the start of the next phase of the cell
cycle. Use examples from both M- and S-cyclin-CDK complexes to explain this.
3. Interpret experimental results of experiments on cyclin-CDK regulation, using examples from the problem
sets as a guide.

This unit covers most of Chapter 18.
• Cell cycle control: pp 613-619 (4th ed. pp 607-613). There are problem set questions associated with the
‘How We Know’ section, so it is worth reading.
• G1 Phase: pp 620-622 (4th ed. pp 613-616)
• S Phase: pp 623-624 (4th ed. pp 616-618)

Introduction: CDK-Cyclin Regulation
• In the first figure shown, describe what the arrow represents in the experiment. What was the major finding
from these experiments?
• Terminology check: What is the difference between the terms MPF, CDK, and cyclin? Make sure you can
define each of these, and describe their relationship to each other.
• Take a look at Figure 18-5. What is the difference between a protein’s activity, and its concentration? How
might activity and concentration be at different levels for the same protein, at a given time?
• Take a look at Figure 18-8 and the table right above it. You do not need to memorize the specific cyclin-
CDK complexes, and names of cyclins/partners. However, notice that there is a diversity of cyclin-CDK
complexes. Why are there several, rather than just one?
• What are the two ways that the activity of a CDK-cyclin complex can be regulated?
Phosphorylation Controls CDK

• Figure 18-10 depicts the activation of a CDK-cyclin complex. Can you hypothesize why inhibitory
phosphates are necessary in the function/activity of CDK-cyclin?
M-CDK Controls Entry into Mitosis & Re-entry into G1

• What checkpoint does M-CDK regulate?
• Based on the experimental results shown in the table, what are the roles of wee1 and cdc25?
• The M-CDK-cyclin complex phosphorylates many other proteins, as listed in the notes. What do all of these
proteins have in common?
• How is it possible that phosphorylation can activate in some cases, and can de-activate in other cases?
Consider the protein structure-function relationship here.
• See Figure 18-17. What is meant by “positive feedback”?
S-CDK Controls Entry & Exit from S-Phase

• What checkpoint does S-CDK regulate?
• Draw a diagram showing how S-CDK is activated, given that you know that it is activated similarly to M-
CDK.
• In the case of both S- and M-CDK, how might they be involved in exit as well as entry into the phase they
control?
Topic 7.3: Mitosis and Cell Division

1. Review the stages of mitosis and relate how the process of mitosis is driven by the activation of proteins by
the mitotic CDK-cyclin complex.
2. Illustrate how the process of mitosis is driven by the activation of proteins by the mitotic CDK-cyclin
complex.
3. Explain the role of the cytoskeleton (and associated motor proteins) during mitosis including how dynamic
instability of microtubules contributes to the formation and function of the mitotic spindle, and the role of
the actin cytoskeleton during cytokinesis.
4. Explain how proteins and DNA interact to further condense the DNA to a mitotic chromosome.
5. Describe how the regulation of cyclin via ubiquitination results in the end of M-phase, and a transition to
the next phase of the cell cycle.
Topic 7.3 Readings from Essential Cell Biology

• M-Phase: Ch 18, pp 624-639 (4th pp 618-633). Includes Panel 18-1

Chromosomes
• What are the three regions of DNA in a chromosome?
• Why do you think sister chromatids are held together after replication but before anaphase?

• Terminology check: Define each of these terms – Chromosome, chromatid, chromatin, centromere,
cohesin, condensing
Mitosis & Cell Division

• What is the difference between mitosis and cytokinesis?
• Stage 1: Prophase (& Prometaphase) – what are the major events happening in this stage?
• How are these processes supported and promoted by dynamic instability of microtubules (Examine Figures
18-23 and 18-24 if you need a hint)?
• What are the types of microtubules involved? Which motor protein types are helping with each type of
spindle fibre? (Examine MBoC Fig 17-30 if you need a hint.)
• Stage 2: Metaphase – what are the major events happening in this stage?
• Why do chromosomes align on the metaphase plate?
• Recall the phenomenon of “treadmilling.” Why is this phenomenon/process particularly important during
metaphase?
• Stage 3: Anaphase – what are the major events happening in this stage?
• Take a look at Figure 18-28. What role does M-CDK play in anaphase?
• What is happening in Anaphase A and Anaphase B? (Examine Fig 18-29 if you need a hint.)
• Which motor protein types are working to separate the sister chromatids from each other?
• Answer the questions in the text about the different motor proteins involved.
• Stage 4: Telophase – what are the major events happening in this stage?
• How do these events compare to the events that the cell undergoes to prepare for mitosis?
• What proteins are involved in nuclear lamina reformation? How does M-CDK get involved here?
• Stage 5: Cytokinesis – what are the major events happening in this stage?
• How do plant and animal cells differ during cytokinesis, and how are they similar?
• What are the roles of the motor proteins involved in cytokinesis?

BIOL200 Prereading Guide

Uploaded by

Document Information

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

BIOL200 Prereading Guide

Uploaded by

Copyright:

Available Formats

BIOL 200 Pre-Reading Guide:

Learning Outcomes & Required Readings

Overall Course Outcomes

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 1 of 24

TABLE OF CONTENTS ................................................................................................................................................................... 2

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 3 of 24

Topic 1.1: Eukaryotic Cells & Organelles

Topic 1.1 Learning Outcomes

Read Topic 1.1 Online Notes or from Essential Cell Biology

Topic 1.2: Microscopy

Topic 1.2 Learning Outcomes

Read Topic 1.2 Online Notes or from Essential Cell Biology

• Unity and Diversity of Cells: pp 1-6 (4th pp 1-5).

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 4 of 24

(Optional Review) Topic 2.0: Macromolecules

Read Topic 2.0 Online Notes or from Essential Cell Biology

Review of Underlying Chemistry

Biological Macromolecules & Chemical Bonds:

Transcription & Translation:

Topic 2.0 Questions to Consider:

(continued next page)

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 5 of 24

Properties of Biological Macromolecules

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 6 of 24

Topic 2.1 Learning Objectives

Read Topic 2.1 Online Notes or from Essential Cell Biology

Topic 2.1 Questions to Consider:

Topic 2.2 The Lipid Bilayer

Topic 2.2 Learning Objectives

Read Topic 2.2 Online Notes or from Essential Cell Biology

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 7 of 24

Topic 2.3: Membrane Proteins

Topic 2.3 Learning Objectives

Read Topic 2.3 Online Notes or from Essential Cell Biology

Topic 2.3 Questions to Consider:

Determining protein location & orientation experimentally

The Plasma Membrane

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 8 of 24

(Optional Review) Topic 3.0 - Nucleic Acids

Topic 3.0 Questions to Consider:

Nucleic Acids as ‘Informational Polymers’

Topic 3.1 Nuclear Structure & Protein Import

Topic 3.1 Learning Objectives

Read Topic 3.1 Online Notes or from Essential Cell Biology

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 9 of 24

The Nucleolus & Nuclear Pores

Protein Targeting to the Nucleus

Topic 3.2 Chromatin & Chromosomes

Topic 3.2 Learning Objectives

Read Topic 3.2 Online Notes or from Essential Cell Biology

Topic 3.2 Questions to Consider:

(continued next page)

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 10 of 24

Topic 3.3: Regulation of Gene Expression

Topic 3.3. Learning Objectives

Read Topic 3.3 Online Notes or from Essential Cell Biology

Topic 3.3 Questions to Consider:

Control of Gene Expression: Transcription Factors

Control of Gene Expression: Post-transcriptional Processing of mRNA

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 11 of 24

Optional Readings from ECB- Transcription & Translation:

Initiation, Elongation & Termination

BIOL200 Pre-Reading Guide (Learning Outcomes & Required Readings) Page 12 of 24

Topic 4.1: Introduction & Protein Import