BIO301: Cell Biology « The Saylor Foundation

100% Cell Biology

Purpose of Course

As you learned in BIO101, the cell is the fundamental unit of life; in fact, the smallest living organisms are composed of a single cell. We have learned that, despite their small size, cells are far from simple, and we have only recently begun to understand just how complex they are. This course will present you with a detailed overview of a cell’s main components and functions. Most of the units will cover topics familiar to you from BIO101, such as mitosis or the cell nucleus, but will explore them in greater depth. The course is roughly organized into four major areas: the cell membrane, cell nucleus, cell cycle, and cell interior. We will approach most of these topics straightforwardly, from a molecular and structural point of view.

Learning Outcomes show close

Upon successful completion of this course, the student will be able to:

Explain what a eukaryotic cell is, identify the components of the cell, and describe how a cell functions.

Explain how cell membranes are formed.

Identify the general mechanisms of transport across cell membranes.

List the different ways in which cells communicate with one another—specifically, via signaling pathways.

Define what the extracellular matrix is composed of in different cells and how the extracellular matrix is involved in forming structures in specific tissues.

List the components of the cell’s cytoskeleton and explain how the cytoskeleton is formed and how it directs cell movements.

Explain the fundamentals of gene expression and describe how gene expression is regulated at the protein level.

Define and explain the major cellular events involved in mitosis and cytokinesis.

Identify the major cellular events that occur during meiosis.

Describe the eukaryotic cell cycle and identify the events that need to occur during each phase of the cell cycle.

Identify all of the major organelles in eukaryotic cells and their respective major functions.

Course Requirements show close

In order to take this course, you must:

√ Have access to a computer.

√ Have continuous broadband Internet access.

√ Have the ability/permission to install plug-ins or software (e.g. Adobe Reader or Flash).

√ Have the ability to download and save files and documents to a computer.

√ Have the ability to open Microsoft files and documents (.doc, .ppt, .xls, etc.).

√ Be competent in the English language.

√ Have completed the following course listed in “The Core Program” of the Biology discipline as a pre-requisite: BIO101: Introduction to Molecular and Cellular Biology

Course Overview Expand Resources Collapse Resources

3 Cell Signaling
3.1 Basic Types of Cell Signaling
3.1.1 Juxtacrine Signaling
3.1.2 Paracrine Signaling
3.1.3 Endocrine Signaling
3.2 Receptors
3.2.1 G Protein-Coupled Receptors (GPCRs)
3.2.2 Receptor Tyrosine Kinases (RTKs)
3.2.3 Cytokine Receptors
3.2.4 Receptor Serine/Threonine Kinases
3.2.5 Guanylyl Cyclase Receptors
3.2.6 TNF (Tumor Necrosis Factor) Receptor Family
3.3 Reversible Phosphorylation
3.3.1 Kinase and Phosphatase Cycle
3.3.2 Serine and Threonine Phosphorylation
3.3.3 Tyrosine Phosphorylation
3.3.4 Regulation of Kinases and Phosphatases
3.3.5 GTPase (Guanosine TriPhosphatase) Cycle
3.3.6 Trimeric G (Guanosine) Protein Cycle
3.4 Secondary Messengers
3.4.1 Cyclic Nucleotides
3.4.2 Lipid-Derived Secondary Messengers
3.4.3 Calcium
3.4.4 Nitric Oxide
3.5 Integrated Signaling Pathways
3.5.1 Light Signal Transduction Inside Photoreceptor Cells
3.5.2 Epinephrine and Norepinephrine Pathways Inside Muscle
3.5.3 MAPK (Mitogen-Activated Protein Kinase) Pathway
3.6 Synaptic Transmission at Neuromuscular Junction

8 Meiosis
8.1 Meiotic Prophase
8.1.1 Leptotene
8.1.2 Zygotene
8.1.3 Pachytene and Chiasma
8.1.4 Diplotene
8.1.5 Diakinesis
8.2 Meiosis I
8.2.1 Metaphase I
8.2.2 Anaphase I
8.3 Meiosis II
8.3.1 Metaphase II
8.3.2 Metaphase II Arrest in Humans
8.3.3 Anaphase II
8.4 Sperm and Oocyte Difference in Meiosis
8.5 The Saylor Foundation's Unit 8 Quiz

9 The Cell Cycle
9.1 General Phases of Cell Cycle
9.1.1 G1 Phase
9.1.2 S phase
9.1.3 G2 Phase
9.1.4 Mitosis
9.1.5 Interphase
9.1.6 G0 Phase
9.2 Meiosis in the Cell Cycle
9.3 Checkpoints of Cell Cycle
9.3.1 G1 Restriction Point
9.3.2 S Phase Restriction Point
9.3.3 G2 Restriction Point
9.4 Cyclins and Cyclin-Dependent Kinases (CDKs)
9.4.1 General Features of Cyclin and CDK
9.4.2 Positive Regulators of CDK and Cyclin Pairs
9.4.3 Negative Regulators of CDK and Cyclin Pairs
9.4.4 Cyclin Degradation
9.5 The Saylor Foundation's Unit 9 Quiz

Unit 1: Review of Basic Concepts

This unit reintroduces concepts you learned in your introductory biology and chemistry courses. It should serve as a refresher for those of you who have not studied these concepts for some time.

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1.1 Biology

Reading: National Center for Biotechnology Information's Bookshelf: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Molecular Composition of Cells”
Link: National Center for Biotechnology Information's Bookshelf: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Molecular Composition of Cells” (HTML)

Instructions: Read the entirety of this chapter, along with all associated figures (Figs. 2.1-2.21). It will cover the material in subunits 1.1.1-1.1.6.

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1.1.1 Amino Acids

Note: This subunit is covered by the reading assigned beneath subunit 1.1. Focus specifically on the “Protein” section.

1.1.2 Four Levels of Protein Structures

Note: This subunit is covered by the reading assigned beneath subunit 1.1. Focus specifically on the “Protein” section

1.1.3 Carbohydrates

Note: This subunit is covered by the reading assigned beneath subunit 1.1. Focus specifically on the “Carbohydrate” section.

1.1.4 ATP

Note: This subunit is covered by the reading assigned beneath subunit 1.1. Focus specifically on the “Nucleic acids” section.

1.1.5 DNA

Note: This subunit is covered by the reading assigned beneath subunit 1.1. Focus specifically on the “Nucleic acids” section

1.1.6 RNA

Note: This subunit is covered by the reading assigned beneath subunit 1.1. Focus specifically on the “Nucleic acids” section

1.2 Chemistry

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell, A Molecular Approach, 2e: “Metabolic Energy”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell, A Molecular Approach, 2e: “Metabolic Energy” (HTML)

Instructions: In “Metabolic Energy,” read the introduction (one paragraph) and the sections entitled “Free Energy and ATP” and “The Generation of Energy from Glucose,” along with all associated figures (Figs. 2.31-2.35). Do not concern yourself with memorizing the reactions. This reading covers the topics outlined in subunits 1.2.1-1.2.4.

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1.2.1 pH

Note: This subunit is covered by the reading assigned beneath subunit 1.2.

1.2.2 First- and Second-Order Reactions

Note: This subunit is covered by the reading assigned beneath subunit 1.2.

1.2.3 Free Energy

Note: This subunit is covered by the reading assigned beneath subunit 1.2. Focus specifically on the “Free Energy and ATP” section.

1.2.4 Chemical Bonds

Note: This subunit is covered by the reading assigned beneath subunit 1.2.

Assessment: The Saylor Foundation's "Unit 1 Quiz"
Link: The Saylor Foundation's "Unit 1 Quiz" (PDF)

Instructions: Please complete this quiz after working through Unit 1. The questions are either multiple choice or matching. When you are done, check your work against the Saylor Foundation's "Unit 1 Quiz Answer Key (PDF)."
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Unit 2: The Cell Membrane

Organisms must be able to maintain homeostasis, or a constant internal environment, in order to survive. Cells achieve homeostasis by creating a barrier to the outside world—a cell membrane—that enables them to protect their internal environment from external forces. In fact, cells “die” when the cell membrane’s integrity is destroyed or compromised. In this unit, you will learn about the membrane and its properties. You will discover that it serves as much more than just a wall—it also transports nutrients, exports waste, carries signals, and much more.

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2.1 Membrane Components

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell, A Molecular Approach, 2e: “Cell Membranes”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell, A Molecular Approach, 2e: “Cell Membranes” (HTML)

Instructions: Read the introduction and the subsections “Membrane Lipids” and “Membrane Proteins,” along with all associated figures and tables (Figs. 2.45-2.48 and Table 2.3). These will cover the material in 2.1-2.3.

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Lecture: UC Berkeley: Professor Randy Schekman’s “Membrane Structures: Lipids”
Link: UC Berkeley: Professor Randy Schekman’s “Membrane Structures: Lipids” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage, and click on “View in iTunes” for item 42 titled Lecture 1 “Membrane Structure: Lipids.” Because the beginning of this, the first lecture of the course, covers irrelevant topics such as office hours, if you can, you should begin viewing the lecture 6 minutes and 30 seconds into the video.

The video will cover the material in 2.1, 2.2, and all inclusive subunits.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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2.1.1 Lipids, Sphingolipids, Glycolipids

Note: This subunit is covered by the reading and video assigned beneath subunit 2.1. Focus specifically on the “Membrane Lipids” and “Membrane Proteins” sections in the reading.

2.1.2 Sterols

Note: This subunit is covered by the reading and video assigned beneath subunit 2.1.

2.1.3 Triglycerides

Note: This subunit is covered by the reading and video assigned beneath subunit 2.1.

2.2 Fluid Mosaic Model

Note: This subunit is covered by the reading and video assigned beneath subunit 2.1.

2.2.1 Bilayer

Note: This subunit is covered by the reading and video assigned beneath subunit 2.1. Focus specifically on the “Membrane Proteins” section in the reading.

2.2.2 Lipid Asymmetry

Note: This subunit is covered by the reading and video assigned beneath subunit 2.1.

2.3 Membrane Proteins

Lecture: UC Berkeley: Professor Randy Schekman’s “Membrane Structures: Proteins”
Link: UC Berkeley: Professor Randy Schekman’s “Membrane Structures: Proteins” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 41, and select “View in iTunes” for Lecture 2: “Membrane Structure: Proteins.” Please view this entire lecture.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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2.3.1 Peripheral Proteins

Note: This subunit is covered by the reading assigned beneath subunit 2.1. Focus specifically on the “Membrane Proteins” section

2.3.2 Integral Proteins

Note: This subunit is covered by the reading assigned beneath subunit 2.1. Focus specifically on the “Membrane Proteins” section

2.4 Membrane Pumps

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Transport of Small Molecules”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Transport of Small Molecules” (Chapter 12) (HTML)

Instructions: Read the entirety of this section, along with all associated figures (Figs.12.15-12.33). This will cover the materials in subunits 2.4-2.7

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Lecture: UC Berkeley: Professor Randy Schekman’s “Membrane Transport: Permeases and Channels”
Link: UC Berkeley: Professor Randy Schekman’s “Membrane Transport: Permeases and Channels” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage, and click on “View in iTunes” for item number 39 titled Lecture 4 “Membrane Transport: Permeases and Channels.” Please view this video in its entirety

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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2.4.1 Primary Transporters

Note: This subunit is covered by the reading assigned beneath subunit 2.4.

2.4.2 Bacteriorhodopsin

Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology, 4e: “Chapter 3: Membrane Proteins”
Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology, 4e: “Chapter 3: Membrane Proteins” (HTML)

Instructions: Scroll down to and read the section titled “Many Integral Proteins Contain Multiple Transmembrane α Helices.”

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2.4.3 ATP-Drive Pumps

Note: This subunit is covered by the reading assigned beneath subunit 2.4. Focus on the “Active Transport Driven by ATP Hydrolysis” section

2.4.4 ABC (ATP-Binding Cassette) Transporters

Note: This subunit is covered by the reading assigned beneath subunit 2.4. Focus on the “Active Transport Driven by ATP Hydrolysis” section and Figure 12.30.ABC transporters are important to the study of bacteria and immunology. You may have heard of “super germs,” or germs that are resistant to many of the antibiotics that doctors give to patients with infections. Super germs are antibiotic-resistant, because they have special ABC transporters that are designed to pump the drug out of the bacteria, reducing or even negating its effects

2.5 Membrane Carriers

Lecture: UC Berkeley: Professor Randy Schekman’s “Membrane Transport: Nucleocytoplasmic Exchange”
Link: UC Berkeley: Professor Randy Schekman’s “Membrane Transport: Nucleocytoplasmic Exchange” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 38 titled Lecture 5 “Membrane Transport: Nucleocytoplasmic Exchange,” and select “View in iTunes” for this lecture. Please view this lecture in its entirety. This will cover the material in subunits 2.5, 2.6, and all inclusive subunits

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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2.5.1 Uniporters, Antiporters, Symporters

Note: This subunit is covered by the reading assigned beneath subunit 2.4 and the video assigned in subunit 2.5. Focus specifically on the “Active Transport Driven by Ion Gradients” section of the reading.

2.5.2 GLUT1 and GLUT4 (GLUcose Transporters)

Note: This subunit is covered by the video assigned in subunit 2.5.

2.6 Membrane Channels

2.6.1 Sodium Channels

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Purves, Augustine, Fitzpatrick, et al.’s (ed.) Neuroscience 2nd Edition: “Chapter 4: The Molecular Structure of Ion Channels”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Purves, Augustine, Fitzpatrick, et al.’s (ed.) Neuroscience 2^nd Edition: “Chapter 4: The Molecular Structure of Ion Channels” (HTML)

Instructions: Read the entire webpage. The reading also covers the topic outlined in subunit 2.6.2.

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2.6.2 Potassium Channels

Note: This topic is covered by the reading assigned beneath subunit 2.6.1

2.6.3 Leak Channels and Membrane Potential

Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology: “Section 15.4: Intracellular Ion Environment and Membrane Potential”
Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology: “Section 15.4: Intracellular Ion Environment and Membrane Potential” (HTML)

Instructions: Scroll down the webpage, and read the section titled “The Membrane Potential in Animal Cells Depends Largely on Resting K⁺ Channels.”

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2.6.4 Water Channel

Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology: “Section 15.8: Osmosis, Water Channels, and the Regulation of Cell Volume”
Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology: “Section 15.8: Osmosis, Water Channels, and the Regulation of Cell Volume” (HTML)

Instructions: Scroll down the webpage, and read the section titled “Water Channels Are Necessary for Bulk Flow of Water across Cell Membranes.”

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2.7 Membrane Physiology

Note: This subunit is covered by the reading assigned beneath subunit 2.4.

2.7.1 Glucose Transport in Intestines

Note: This subunit is covered by the reading assigned beneath subunit 2.4. Focus specifically on the “Active Transport Driven by Ion Gradients” section.

2.7.2 Synthesis of ATP in Mitochondria

Note: This subunit is covered by the reading assigned beneath subunit 2.4. Focus specifically on the “Active Transport Driven by ATP Hydrolysis” section.

Assignment: Assignment for Unit 2: University of Arizona’s Biology Project: “Cell Biology”
Link: University of Arizona’s Biology Project: “Cell Biology” (HTML)

Instructions: In the “Cell Membranes” tutorial, answer questions 1-13.

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Unit 3: Cell Signaling

Cells must be able to adapt to changes in the external environment. Cells in multicellular organisms must even be able to communicate with one another and cooperate in order to carry out functions. In fact, all of your body’s activities (from flexing a muscle to releasing stomach acid) rely on cellular communication or cell signaling. In this unit, we will discuss the ways in which cells talk to one another and respond to the environment. Note that this is a large and complex unit with a number of new terms.

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3.1 Basic Types of Cell Signaling

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Signaling Molecules and Their Receptors”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.:Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Signaling Molecules and Their Receptors” (HTML)

Instructions: Read the introduction and the subsection “Modes of Cell-Cell Signaling.” This resource will cover the topics outlined in subunits 3.1.2 and 3.1.3.

Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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Lecture: UC Berkeley: Professor Randy Schekman’s “Cell Communication”
Link: UC Berkeley: Professor Randy Schekman’s “Cell Communication” (YouTube)

Also available in:
iTunes U

Instructions: Watch Lecture 30 (“Cell Communication: ligand and receptors”).

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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3.1.1 Juxtacrine Signaling

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: S.F. Gilbert’s Developmental Biology, 6e: “Juxtracrine Signaling”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: S.F. Gilbert’s Developmental Biology, 6e: “Juxtracrine Signaling” (HTML)

Instructions: Read the introduction and the section titled “The Notch Pathway: Juxtaposed Ligands and Receptors.”

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3.1.2 Paracrine Signaling

Note: This subunit is covered by the reading assigned beneath subunit 3.1.

3.1.3 Endocrine Signaling

Note: This subunit is covered by the reading assigned beneath subunit 3.1.

3.2 Receptors

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Functions of Cell Surface Receptors”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.:Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Functions of Cell Surface Receptors” (HTML)

Instructions: Read the entirety of the section. This will cover the material in 3.2-3.3.

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Lecture: UC Berkeley: Professor Kunxin Luo’s “Receptors”
Link: UC Berkeley: Professor Kunxin Luo’s “Receptors”

Also available in:
iTunes U

Instructions: Scroll down to item 13 titled Lecture 31: “Receptors,” and click on “View in iTunes.” Please watch this lecture in its entirety.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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3.2.1 G Protein-Coupled Receptors (GPCRs)

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “G Protein-Coupled Receptors” section.

Lecture: UC Berkeley: Professor Kunxin Luo’s “G-Protein-Coupled Receptor Signaling I”
Link: UC Berkeley: Professor Kunxin Luo’s “G-Protein-Coupled Receptor Signaling I” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 12 titled Lecture 32: “G Protein Receptor Signaling I,” and click on “View in iTunes.” Please watch the lecture in its entirety.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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3.2.2 Receptor Tyrosine Kinases (RTKs)

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the "Receptor Protein-Tyrosine Kinases” section.

Lecture: UC Berkeley: Professor Kunxin Luo’s “Receptor Tyrosine Kinase Signaling”
Link: UC Berkeley: Professor Kunxin Luo’s “Receptor Tyrosine Kinase Signaling” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 10 titled Lecture 34: “Receptor Tyrosine Kinase Signaling,” and click on “View in iTunes.” Please watch the video in its entirety.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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3.2.3 Cytokine Receptors

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Cytokine Receptors and Nonreceptor Protein-Tyrosine Kinases” section.

3.2.4 Receptor Serine/Threonine Kinases

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Receptors Linked to Other Enzymatic Activities” section.

3.2.5 Guanylyl Cyclase Receptors

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Receptors Linked to Other Enzymatic Activities” section

3.2.6 TNF (Tumor Necrosis Factor) Receptor Family

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Receptors Linked to Other Enzymatic Activities” section. What we now call the TNF family of receptors was first identified as a single receptor capable of inducing death in cancer cells (hence the name—necrosis means “death”). Since then, researchers have discovered a number of similar receptors, all of which have cancer-fighting properties.

3.3 Reversible Phosphorylation

3.3.1 Kinase and Phosphatase Cycle

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Receptors Linked to Other Enzymatic Activities” section

3.3.2 Serine and Threonine Phosphorylation

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Receptors Linked to Other Enzymatic Activities” section

3.3.3 Tyrosine Phosphorylation

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Receptors Linked to Other Enzymatic Activities” section

3.3.4 Regulation of Kinases and Phosphatases

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “Receptors Linked to Other Enzymatic Activities” section

3.3.5 GTPase (Guanosine TriPhosphatase) Cycle

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “G Protein-Coupled Receptors” section

3.3.6 Trimeric G (Guanosine) Protein Cycle

Note: This subunit is covered by the reading assigned beneath subunit 3.2. Focus on the “G Protein-Coupled Receptors” section

3.4 Secondary Messengers

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Pathways of Intracellular Transduction”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Pathways of Intracellular Transduction” (HTML)

Instructions: Read the introduction and the subsections “cAMP Pathway,” “Cyclic GMP,” "Phospholipids and Ca2+”, and “Ras, Raf, and the MAP Kinase Pathway.” These will cover the materials in 3.4-3.5.

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3.4.1 Cyclic Nucleotides

Note: This subunit is covered by the reading assigned beneath subunit 3.4. Focus on the “cAMP Pathway: Second Messengers and Protein Phosphorylation” and “Cyclic GMP” sections. Cyclic nucleotides refer mainly to cAMP and cGMP, both of which are created by specific cyclase enzymes.

3.4.2 Lipid-Derived Secondary Messengers

Note: This subunit is covered by the reading assigned beneath subunit 3.4. Focus on the “Phospholipids and Ca2+” section. You should know the following important classes of lipid-derived secondary messengers: phosphatidylinositol (PI), phosphatidylcholine (PC), and sphingomyelin. Each of these classes has its own set of messengers. The PI class, for example, includes inositol triphosphate (IP3) and diacylglycerol (DAG), among others.

3.4.3 Calcium

Note: This subunit is covered by the reading assigned beneath subunit 3.4. Focus on the “Phospholipids and Ca²⁺” section.

3.4.4 Nitric Oxide

Note: This subunit is covered by the reading assigned beneath subunit 3.4. Focus on the “Cyclic GMP” section

3.5 Integrated Signaling Pathways

Note: This subunit is covered by the reading assigned beneath subunit 3.4.

3.5.1 Light Signal Transduction Inside Photoreceptor Cells

Note: This subunit is covered by the reading assigned beneath subunit 3.4. Focus on the “Cyclic GMP” section.

3.5.2 Epinephrine and Norepinephrine Pathways Inside Muscle

Note: This subunit is covered by the reading assigned beneath subunit 3.4. Focus on the “cAMP Pathway: Second Messengers and Protein Phosphorylation” section.

3.5.3 MAPK (Mitogen-Activated Protein Kinase) Pathway

Note: This subunit is covered by the reading assigned beneath subunit 3.4. Focus on the “Ras, Raf, and the MAP Kinase Pathway” section

Lecture: UC Berkeley: Professor Kunxin Luo’s “The Ras-MAP Kinase Pathway”
Link: UC Berkeley: Professor Kunxin Luo’s “The Ras-MAP Kinase Pathway” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 9 titled Lecture 35: “The Ras-MAP Kinase Pathway,” and select “View in iTunes.” Please watch this entire video lecture.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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3.6 Synaptic Transmission at Neuromuscular Junction

Lecture: UC Berkeley: Professor Randy Schekman’s “Synaptic Transmission”
Link: UC Berkeley: Professor Randy Schekman’s “Synaptic Transmission” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item number 29 titled Lecture 13: “Synaptic Transmission,” and select “View in iTunes.” Please watch this entire video lecture.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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Assignment: Assignment for Unit 3: University of Arizona’s Biology Project: “Cell Biology”
Link: University of Arizona’s Biology Project: “Cell Biology” (HTML)

Instructions: In the “Cell Signaling” tutorial, answer questions 1-4 and 6-12.

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Assessment: The Saylor Foundation's "Unit 3 Quiz"
Link: The Saylor Foundation's "Unit 3 Quiz" (PDF)

Instructions: Please complete this quiz after working through Unit 3. The questions are either multiple choice or matching. When you are done, check your work against the Saylor Foundation's "Unit 3 Quiz Answer Key” (PDF).
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Unit 4: The Extracellular Matrix (ECM)

Different types of cells produce and secrete different molecules that can alter their external environment. An environment that has been altered in this way is known as the extracellular matrix. The matrix’s main purpose is to form an ordered network for physical support, but it also plays a role in signaling, immunity, and wound healing. There are five main classes of ECM molecules; all ECMs are comprised of some combination of these five types.

Unit 4 Time Advisory show close

Unit 4 Learning Outcomes show close

4.1 ECM Molecules

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Cell Walls and the Extracellular Matrix”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Cell Walls and the Extracellular Matrix” (HTML)

Instructions: Read the subsection “The Extracellular Matrix,” along with all associated figures (Figs. 12.51-12.61). This reading covers the topics outlined in subunits 4.1, 4.2, and all inclusive subunits.

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4.1.1 Collagen

Note: This subunit is covered by the reading assigned beneath subunit 4.1. Focus on Figures 12.52 –12.55 and Table 12.2.

4.1.2 Elastic Fibers

Note: This subunit is covered by the reading assigned beneath subunit 4.1.

4.1.3 Proteoglycans

Note: This subunit is covered by the reading assigned beneath subunit 4.1. Focus on Figure 12.57.

4.1.4 Hyaluronan

Note: This subunit is covered by the reading assigned beneath subunit 4.1. Focus on Figure 12.57.

4.1.5 Adhesive Glycoproteins

Note: This subunit is covered by the reading assigned beneath subunit 4.1

4.2 Basal Lamina

Note: This subunit is covered by the reading assigned beneath subunit 4.1. Focus on Figure 12.51.

4.3 Cellular Adhesion

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Cell-Cell Interactions”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Cell-Cell Interactions” (HTML)

Instructions: Read the introduction and the subsections “Cell Adhesion Proteins,” “Tight Junctions,” and “Gap Junctions” and click on all associated figures and tables (Figs. 12.62-12.66 and Table 12.3). These will cover the material in 4.3-4.4.

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Lecture: UC Berkeley: Professor David G. Drubin’s “Cell Adhesion, Motility, and Division”
Link: UC Berkeley: Professor David G. Drubin’s “Cell Adhesion, Motility, and Division” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down to item 22 titled Lecture 21: “Cell Adhesion, Motility, and Division,” and select “View in iTunes.” Please watch this entire video lecture, which covers subunits 4.3, 4.4, and all inclusive subunits.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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4.3.1 Cell Adhesion Molecules (CAMs)

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Cell Adhesion Proteins” section and Figures 12.62-12.64 and Table 12.3

4.3.2 Immunoglobulin CAM (Ig-CAM)

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Cell Adhesion Proteins” section.

4.3.3 Cadherin Family

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Cell Adhesion Proteins” section and Figure 12.64.

4.3.4 Integrin Family

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Cell Adhesion Proteins” section.

4.3.5 Selectin Family

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Cell Adhesion Proteins” section.

4.4 Intercellular Junctions

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3.

4.4.1 Tight Junctions

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Tight Junctions” section and Figure 12.65.

4.4.2 Gap Junctions

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Gap Junctions” section and Figure 12.66.

4.4.3 Adherens Junctions and Desmosomes

Note: This subunit is covered by the reading and video assigned beneath subunit 4.3. Focus on the “Cell Adhesion Proteins” section.

4.5 ECM and Connective Tissue

4.5.1 Loose Connective Tissue (LCT)

Note: This subunit is covered by the reading and video assigned beneath subunit 4.1. Focus on the “The Extracellular Matrix” section. There are substantial differences between loose and dense connective tissue. Dense tissue is largely comprised of collagen (type I), while loose connective tissue has as equalamounts of elastic fibers and collagen. DCT makes up ligaments and tendons, while LCT surrounds nearly every internal organ in the body.

4.5.2 Dense Connective Tissue (DCT)

Reading: National Center for Biotechnology Information’s Bookshelf: B. Alberts, et al.’s Molecular Biology of the Cell, 4e “The Extracellular Matrix of Animals”
Link: National Center for Biotechnology Information’s Bookshelf: B. Alberts, et al.’s Molecular Biology of the Cell, 4e “The Extracellular Matrix of Animals” (HTML)

Instructions: Scroll down the webpage a little more than half-way, and read the section titled “Cells Help Organize the Collagen Fibrils They Secrete by Exerting Tension on the Matrix,” as well as view the associated figure.

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Unit 5: The Cytoskeleton

The cytoskeleton, as the name suggests, provides the physical support for the interior of the cell. You might think of it as “cellular skeleton.” There are three main types of support molecules: actin, tubulin, and intermediate filaments. All the muscles fibers in your body are mainly composed of these support molecules. These molecules also build an internal highway within the cell, upon which almost everything is transported. This unit will explore all three molecules in detail and provide some important examples of what they combine to create.

Unit 5 Time Advisory show close

Unit 5 Learning Outcomes show close

Assignment: University of Arizona’s Biology Project: “Cell Biology”
Link: University of Arizona’s Biology Project: “Cell Biology” (HTML)

Instructions: In the “Cytoskeleton” tutorial, under “Test Yourself (5 problems)”, answer questions 1 and 3-5.

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5.1 Cytoskeleton Molecules

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Cytoskeleton and Cell Movement”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Cytoskeleton and Cell Movement” (HTML)

Instructions: Read the introduction. This will cover the material in subunits 5.1.1-5.1.3.

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Lecture: UC Berkeley: Professor David G. Drubin’s “Actin Filaments: Structural and Dynamic Properties”
Link: UC Berkeley: Professor David G. Drubin’s “Actin Filaments: Structural and Dynamic Properties” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 26 titled Lecture 17: “Actin Filaments: Structural and Dynamic Properties,” and click on “View in iTunes.” Please watch the video in its entirety, which will also cover the topics outlined in subunits 5.1.1-5.1.3.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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5.1.1 Actin

Note: This subunit is covered by the reading and video assigned beneath subunit 5.1.

5.1.2 Tubulin

Note: This subunit is covered by the reading and video assigned beneath subunit 5.1.

5.1.3 Intermediate Filaments

Note: This subunit is covered by the reading and video assigned beneath subunit 5.1.

5.2 Actin Family

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Structure and Organization of Actin Filaments”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Structure and Organization of Actin Filaments” (HTML)

Instructions: Read the introduction and subsections “Assembly and Disassembly,” “Organization,” and “Association of Actin Filaments” along with all associated figures (Figs. 11.1-11.14). These will cover the material in 5.2.1-5.2.5 and 5.5.1.

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Lecture: UC Berkeley: Professor Randy Schekman’s “Actin-Binding Proteins and Cell Migration”
Link: UC Berkeley: Professor Randy Schekman’s “Actin-Binding Proteins and Cell Migration” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 25 titled Lecture 18: “Actin Binding Proteins and Cell Migration,” and click on “View in iTunes.” Please watch this entire video lecture, which also covers the topics outlined in subunit 5.5.1.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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5.2.1 Actin Polymerization

Note: This subunit is covered by the reading and video assigned beneath subunit 5.2. Focus on the “Assembly and Disassembly of Actin Filaments” section and Figures 11.2 and 11.3.

5.2.2 Actin Binding Proteins

Note: This subunit is covered by the reading and video assigned beneath subunit 5.2. Focus on the “Assembly and Disassembly of Actin Filaments” section and Figure 11.5.

5.2.3 Actin Filament Capping Proteins

Note: This subunit is covered by the video assigned beneath subunit 5.2.

5.2.4 Actin Filament Severing Proteins

Note: This subunit is covered by the video assigned beneath subunit 5.2.

5.2.5 Actin Filament Cross-Linking (or “Bundling”) Proteins

Note: This subunit is covered by the reading and video assigned beneath subunit 5.2. Focus on the “Organization of Actin Filaments” section and Figure 11.6.

5.3 Tubulin

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Microtubules”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Microtubules” (HTML)

Instructions: Read the introduction and subsections “Structure, Assembly, and Dynamic Instability” and “Stabilization of Microtubules,” along with all associated figures (Figs. 11.37, 11.38, and 11.44). These will cover the material in 5.3.1-5.3.3.

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Lecture: UC Berkeley: Professor David G. Drubin’s “Microtubules: Structure and Dynamic Properties”
Link: UC Berkeley: Professor David G. Drubin’s “Microtubules: Structure and Dynamic Properties” (YouTube)

Also available in:
Tunes U

Instructions: Scroll down the webpage to item 20 titled Lecture 23: “Microtubules: Structure and Dynamic Properties,” and click on “View in iTunes.” Please watch this entire video lecture

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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5.3.1 Microtubule Assembly from GTP Tubulin

Note: This subunit is covered by the reading and video assigned beneath subunit 5.3. Focus on the “Structure, Assembly, and Dynamic Instability of Microtubules” section and Figure 11.38.

5.3.2 Microtubule Associated Proteins

Note: This subunit is covered by the reading and video assigned beneath subunit 5.3. Focus on the “Stabilization of Microtubules and Cell Polarity” section.

5.3.3 Microtubule Destabilizing and Stabilizing Proteins

Note: This subunit is covered by the reading and video assigned beneath subunit 5.3. Focus on the “Stabilization of Microtubules and Cell Polarity” section.

5.4 Intermediate Filaments

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Intermediate Filaments”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Intermediate Filaments” (HTML)

Instructions: Read the introduction and the subsection “Intermediate Filament Proteins,” along with Figure 11.31. These will cover the material in 5.4.1-5.4.4.

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Lecture: UC Berkeley: Professor David G. Drubin’s “Intermediate Filaments and Septins”
Link: UC Berkeley: Professor David G. Drubin’s “Intermediate Filaments and Septins” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down to item 21 titled Lecture 22: “Intermediate Filaments and Septins,” and click on “View in iTunes.” Please watch this entire video lecture.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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5.4.1 Rod Domains

Note: This subunit is covered by the reading and video assigned beneath subunit 5.4.

5.4.2 Lamins

Note: This subunit is covered by the reading and video assigned beneath subunit 5.4.

5.4.3 Desmins

Note: This subunit is covered by the reading and video assigned beneath subunit 5.4.

5.4.4 Keratins

Note: This subunit is covered by the reading and video assigned beneath subunit 5.4.

5.5 Cytoskeletal Models

Note: This topic is covered by the materials linked in the inclusive subunits below.

5.5.1 Treadmilling

Note: This subunit is covered by the reading and video assigned beneath subunit 5.2. Focus on the “Assembly and Disassembly of Actin Filaments” section and Figure 11.4.Treadmilling is a process in which actin and tubulin units appear to be “walking.” This occurs when individual units fall off one end (the minus end) while units add to the other end (the plus end), resulting in a motion that resembles walking.

5.5.2 Filopodia and Lamellipodia

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Actin, Myosin, and Cell Movement”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Actin, Myosin, and Cell Movement” (HTML)

Instructions: Read the subsection entitled “Cell Crawling.”

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5.5.3 Desmosomes and Hemidesmosomes

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Intermediate Filaments”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Intermediate Filaments” (HTML)

Instructions: Read the subsection “Intracellular Organization of Intermediate Filaments,” along with Figure 11.34.

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5.5.4 Skeletal Muscle Filament

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Actin, Myosin, and Cell Movement”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Actin, Myosin, and Cell Movement” (HTML)

Instructions: Read the subsection entitled “Muscle Contraction.”

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5.5.5 Kinesin-Dynein

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Microtubule Motors and Movements”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Microtubule Motors and Movements” (HTML)

Instructions: Read the introduction and subsections “Identification of Microtubule Motor Proteins,” “Organelle Transport,” and “Cilia and Flagella,” along with all associated figures (Figs. 11.45-11.47 and 11.50-11.53). These will cover the material in subsections 5.5.5-5.5.7.

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5.5.6 Flagella

Note: This subunit is covered by the reading assigned beneath subunit 5.5.5. Focus specifically on the “Cilia and Flagella” section of the reading.

5.5.7 Cilia

Note: This subunit is covered by the reading assigned beneath subunit 5.5.5. Focus specifically on the “Cilia and Flagella” section of the reading.

Assignment: Assignment for Unit 5: University of Arizona’s Biology Project: “Cell Biology”
Link: University of Arizona’s Biology Project: “Cell Biology” (HTML)

Instructions: In the “Cytoskeleton” tutorial, under “Test Yourself (5 problems)”, answer questions 1 and 3-5.

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The Saylor Foundation's Unit 5 Quiz

Assessment: The Saylor Foundation's "BIO301 Unit 5 Quiz"
Link: The Saylor Foundation's "BIO301 Unit 5 Quiz" (PDF)

Instructions: Please complete the linked quiz to test your knowledge of the material covered in Unit 5. When you are done, check your work against The Saylor Foundation's "BIO301 Unit 5 Quiz Answer Key” (PDF).
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Unit 6: The Cell Nucleus and Gene Expression

As you learned in BIO101, the cell nucleus is the storage area for all genetic material and constantly full of activity. The nucleus in fact contains not only DNA, but RNA and protein as well. This unit will take a detailed look at chromosomes, the cell nucleus, gene expression, and expression regulation. When we refer to “expression regulation,” we are talking about the fact that not all genes are expressed in the cell at the same time. After all, though a liver cell and a nerve cell have the same genome (and thus the same DNA), they look and act completely differently. How does this happen? The answer is regulated gene expression!

Unit 6 Time Advisory show close

Unit 6 Learning Outcomes show close

6.1 Chromosome Organization

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Chromosomes and Chromatin” “Chromosomes and Chromatin”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Chromosomes and Chromatin” “Chromosomes and Chromatin” (HTML)

Instructions: Read the introduction and subsection “Chromatin,” along with Table 4.3 and all associated figures (Figs. 4.8-4.14). This will cover the material in 6.1.1-6.1.6.

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Lecture: iTunes U: UC Berkeley: Professor David G. Drubin’s “Nuclear and Chromatin Structure”
Link: iTunes U: UC Berkeley: Professor David G. Drubin’s “Nuclear and Chromatin Structure” (iTunes U)

Instructions: Scroll down the webpage to item 18 titled Lecture 25: “Nuclear and Chromatin Structure,” and click on “View in iTunes.” Please watch this video lecture in its entirety. Please note that the first few minutes of the video lecture deals with class administration issues and will not be necessary to view. This material covers the topics outlined in 6.1, 6.2, and all inclusive subunits.

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6.1.1 DNA and Histones

Note: This subunit is covered by the reading assigned beneath subunit 6.1.

6.1.2 Nucleosome

Note: This subunit is covered by the reading assigned beneath subunit 6.1.

6.1.3 30-nm Fiber

Note: This subunit is covered by the reading assigned beneath subunit 6.1.

6.1.4 Loop Domain Model

Note: This subunit is covered by the reading assigned beneath subunit 6.1.

6.1.5 Nuclear Scaffolding

Note: This subunit is covered by the reading assigned beneath subunit 6.1.

6.1.6 Euchromatin and Heterochromatin

Note: This subunit is covered by the reading assigned beneath subunit 6.1. Be sure to remember that euchromatin is for active gene use and heterochromatin is for genes that are inactivated or not in use.

6.2 Nuclear Organization

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Nuclear Envelope and the Traffic between the Nucleus and Cytoplasm”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Nuclear Envelope and the Traffic between the Nucleus and Cytoplasm” (HTML)

Instructions: Read the introduction and subsections “Structure of the Nuclear Envelope”, “The Nuclear Pore Complex,” and “Selective Transport of Proteins to and from the Nucleus” along with all associated figures (Figs. 8.1-8.11). These will cover the materials in 6.2.1.-6.2.4.

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6.2.1 Inner and Outer Membrane

Note: This subunit is covered by the reading assigned beneath subunit 6.2. Focus on Figure 8.1.

6.2.2 Nuclear Pores

Note: This subunit is covered by the reading assigned beneath subunit 6.2. Focus on Figure 8.2.

6.2.3 Nucleoplasm

Note: This subunit is covered by the reading assigned beneath subunit 6.2. Focus on Figure 8.8.

6.2.4 Nuclear Lamina

Note: This subunit is covered by the reading assigned beneath subunit 6.2. Focus on Figure 8.4.

6.2.5 Nucleolus

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Nucleolus”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Nucleolus” (HTML)

Instructions: Read the introduction and the subsection “Ribosomal RNA Genes and the Organization of the Nucleolus,” along with all associated figures (Figs. 8.22-8.24).

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6.3 Gene Expression Transcription Unit

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Eukaryotic RNA Polymerases and General Transcription Factors”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Eukaryotic RNA Polymerases and General Transcription Factors” (HTML)

Instructions: Read the introduction and subsections “Eukaryotic RNA Polymerases” and “General Transcription Factors and the Initiation of Transcription by RNA Polymerase II,” along with all associated figures (Figs. 6.12-6.14). This will cover the material in 6.3.1-6.3.5.

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Lecture: MIT OpenCourseware: Professor Graham Walker’s “Lecture 13: Gene Regulation I”
Link: MIT OpenCourseware: Professor Graham Walker’s “Lecture 13: Gene Regulation I” (YouTube)

Also available in:
MPEG4 (MP4) and OGG
iTunes U Video, and Transcript

Instructions: Watch the entire video lecture (about 50 minutes) on MIT’s Opencourseware website. You may also click on the tab titled “Transcript” to read the transcript in HTML or to click on “Download” to access the PDF file. This lecture will cover the topics outlined in subunits 6.3.1-6.3.3

Terms of Use: Graham Walker, 7.014 Introductory Biology, Spring 2005. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed January 11, 2011). License: Creative Commons BY-NC-SA 3.0. The original version can be found here.
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6.3.1 RNA Polymerase II

Note: This subunit is covered by the reading and video assigned beneath subunit 6.3

6.3.2 General Transcription Factors

Note: This subunit is covered by the reading and video assigned beneath subunit 6.3. Focus on “General Transcription Factors and Initiation of Transcription by RNA Polymerase II” section of the reading.

6.3.3 DNA Binding Domains

Note: This subunit is covered by the reading and video assigned beneath subunit 6.3.

6.3.4 RNA Maturation

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Translation of mRNA” and “RNA Processing and Turnover”
Links: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Translation of mRNA” and “RNA Processing and Turnover” (HTML)

Instructions: From “Translation of RNA,” read the introduction and the subsections “The Ribosome,” “Organization of mRNAs” (first paragraph only), and “The Process of Translation,” along with associated figures (Figs. 7.4-7.6 and 7.8-7.14). Read the section “RNA Processing and Turnover” in its entirety, along with all associated figures (Figs. 6.37-6.38). These will cover the material in 6.3.5-6.3.7.

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6.3.5 Ribosome

Note: This subunit is covered by the reading assigned beneath subunit 6.3.4. Focus on “Translation of mRNA.”

6.3.6 Translation

Note: This subunit is covered by the reading assigned beneath subunit 6.3.4. Focus on “Translation of mRNA.”

6.3.7 Protein Folding

Note: This subunit is covered by the reading assigned beneath subunit 6.3.4.

6.4 Regulation of Gene Expression

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: “Regulation of Transcription in Eukaryotes”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: “Regulation of Transcription in Eukaryotes” (HTML)

Instructions: Read this section in its entirety, along with all associated figures (Figs. 6.18-6.36). This will cover the material in 6.4.1-6.4.4. Please note that, although they are not described as such, the “Relationship of Chromatin Structure to Transcription” and “DNA Methylation” are examples of epigenetic regulation.

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Lecture: MIT OpenCourseware: Professor Graham Walker’s “Lecture 14: Gene Regulation II”
Link: MIT OpenCourseware: Professor Graham Walker’s “Lecture 14: Gene Regulation II” (YouTube)

Also available in:
MPEG4 (MP4) and OGG
iTunes U Video, and Transcript

Instructions: Watch the entire video lecture (about 47:30 minutes) on MIT’s Opencourseware website. You may also click on the tab titled “Transcript” to read the transcript in HTML or to click on “Download” to access the PDF file. Please note that this lecture also covers the topics outlined in subunits 6.4.1-6.4.4.

Terms of Use: Graham Walker, 7.014 Introductory Biology, Spring 2005. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed January 11, 2011). License: Creative Commons BY-NC-SA 3.0. The original version can be found here.
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6.4.1 Epigenetic Regulation

Note: This subunit is covered by the reading and video assigned beneath subunit 6.4. Focus on the “Relationship of Chromatin Structure to Transcription” and “DNA Methylation” sections of the reading.

6.4.2 Post-transcriptional Modifications

Note: This subunit is covered by the reading and video assigned beneath subunit 6.4.

6.4.3 Repressors and Enhancers

Note: This subunit is covered by the reading and video assigned beneath subunit 6.4. Focus on “Eukaryotic Repressors” and cis-Acting Regulatory Sequences: Promoters and Enhancers” sections of the reading.

6.4.4 Inducible Systems

Note: This subunit is covered by the reading and video assigned beneath subunit 6.4. Focus on “Structure and Function of Transcriptional Activators” section.

Assignment: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Questions - The Nucleus” and “Questions – RNA Synthesis and Processing”
Links: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Questions - The Nucleus” and “Questions – RNA Synthesis and Processing” (both HTML)

Instructions: Answer all questions (1-5). Please note that answers are posted directly below the questions asked; try to cover them while you answer the questions yourself.

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Web Media: Studio Daily: XVIVO and Harvard University’s “The Inner Life of a Cell”
Link: Studio Daily: XVIVO and Harvard University’s “The Inner Life of a Cell” (Flash)

Instructions: Please note that this resource is optional. Watch this short (eight-minute), un-narrated video to visualize the processes occurring daily within a eukaryotic cell. This video was created by animators as XVIVO after consultation with cell and molecular biologists at Harvard University, in order to illustrate the workings of a cell.

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The Saylor Foundation's Unit 6 Quiz

Assessment: The Saylor Foundation's "BIO301 Unit 6 Quiz"
Link: The Saylor Foundation's "BIO301 Unit 6 Quiz" (PDF)

Instructions: Please complete the linked quiz to test your knowledge of the material covered in Unit 6. When you are done, check your work against The Saylor Foundation's "BIO301 Unit 6 Quiz Answer Key” (PDF).
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Unit 7: Mitosis and Cytokinesis

Every cell in your body has the capacity to divide and make new cells. Mitosis is the process by which one cell turns into two identical ones. Because of mitosis, most cells in your body don’t live past a few months. In other words, despite your chronological age, your body is really just a few months old!

Mitosis is split into four phases. This unit will carefully explore each phase, ending with cytokinesis, whereby the cell membrane will pinch itself off and split in half in order to produce two separate cells.

Unit 7 Time Advisory show close

Unit 7 Learning Outcomes show close

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell: A Molecular Approach: “The Events of M Phase”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: Professor Geoffrey Cooper’s The Cell: A Molecular Approach: “The Events of M Phase” (HTML)

Instructions: Read the section in its entirety, along with all associated figures (Figs. 14.23-14.31). This reading will cover the topics outlined in subunits 7.1-7.7, and all inclusive subunits.

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Lecture: UC Berkeley: Professor David G. Drubin’s “Mitosis and Cell Division”
Link: UC Berkeley: Professor David G. Drubin’s “Mitosis and Cell Division” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 17 titled Lecture 26: “Mitosis and Cell Division,” and click on “View in iTunes.” Please watch the entire video lecture. Note that this lecture covers topics outlined in subunits 7.1-7.7, and all inclusive subunits.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Professor Harvey Lodish et al.’s Molecular Cell Biology, 4e: “Microtubule Dynamics and Motor Proteins during Mitosis.”
Link:Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Professor Harvey Lodish et al.’s Molecular Cell Biology, 4e: “Microtubule Dynamics and Motor Proteins during Mitosis.”

Instructions: Read the section in its entirety, along with associated figures. This will cover material in subunits 7.2-7.7.

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7.1 Open Mitosis and Closed Mitosis

Note: This subunit is covered by the Cooper reading and video assigned beneath the Unit 7 introduction.

7.2 Prophase

Note: This subunit is covered by the reading and video assigned beneath the Unit 7 introduction. Focus on the “Stages of Mitosis” section of the reading.

7.2.1 Nuclear Condensation and Condensin

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. Focus on the “MPF and Progression to Metaphase” section of the reading. This subunit is covered by the Lodish reading assigned beneath Unit 7. Focus on the first section and the “The Kinetochore is a specialized attachment site at the chromosome centromere” section.

7.2.2 Cytoplasmic Changes

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. Focus on the “MPF and Progression to Metaphase” section of the reading.

7.3 Prometaphase

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. This subunit is covered by the Lodish reading assigned beneath Unit 7. Focus on the “Kinetichores generate the force for poleward chromosome movement” section.

7.3.1 Nuclear Envelope

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. Focus on the “MPF and Progression to Metaphase” section of the reading. This subunit is covered by the Lodish reading assigned beneath Unit 7. Focus on the “Astral Microtubules determine where cytokinesis takes place” section.

7.3.2 Spindle Assembly

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. This subunit is covered by the Lodish reading assigned beneath Unit 7. Focus on the “Formation of poles and capture of chromosomes are key events in spindle assembly” section.

7.3.3 Chromosome Attachment

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. Focus on the “Stages of Mitosis” section of the reading. This subunit is covered by the Lodish reading assigned beneath Unit 7. Focus on the “The kinetochore is a specialized attachment site at the chromosome centromere” section.

7.4 Metaphase

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. Focus on the “MPF and Progression to Metaphase” section of the reading. This subunit is also covered by the Lodish reading assigned beneath Unit 7.

7.4.1 Metaphase Plate

7.4.2 Chromosomal Oscillations and Microtubule Flux

Note: This subunit is also covered by the Lodish reading assigned beneath Unit 7. Focus on the section titled “Kinetochores Generate the Force for Poleward Chromosome Movement."

7.5 Anaphase

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. Focus on the “Proteolysis and the Inactivation of MPF: Anaphase and Telophase” section of the reading. This subunit is also covered by the Lodish reading assigned beneath Unit 7. Focus on the “During Anaphase chromosomes separate and the spindle elongates” section.

7.5.1 Anaphase A

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. This subunit is also covered by the Lodish reading assigned beneath Unit 7. Focus on the “Microtubule shortening during Anaphase A” section.

7.5.2 Anaphase B

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7 This subunit is also covered by the Lodish reading assigned beneath Unit 7. Focus on the “Spindle elongation during anaphase B” section. Anaphase A is the earlier of the two anaphase phases, when there is a shortening of the microtubules but no actual separation of chromosomes or ATP usage. Anaphase B refers to the process of separating the two poles of chromosomes; it also requires ATP for energy

7.6 Telophase

7.7 Cytokinesis

Note: This subunit is covered by the Cooper reading and video assigned beneath Unit 7. Focus on the “Cytokinesis” section of the reading. This subunit is also covered by the Lodish reading assigned beneath Unit 7.

7.7.1 Contractile Ring

7.7.2 Variations in Bacteria

Reading: David Krogh’s Biology, A Guide to the Natural World: “Introduction to Genetics, Mitosis, and Cytokinesis”
Link: Prentice Hall: David Krogh’s Biology, A Guide to the Natural World: “Introduction to Genetics, Mitosis, and Cytokinesis” (HTML)

Instructions: Read subsection 9.5, “Variations in Cell Division.”

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Assignment: Assignment for Unit 7: University of Arizona’s Biology Project: “Cell Biology”
Link: University of Arizona’s Biology Project: “Cell Biology” (HTML)

Instructions: In the “Cell Cycle and Mitosis” tutorial, under “Test Yourself (11 problems)”, answer questions 1-11.

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The Saylor Foundation's Unit 7 Quiz

Assessment: The Saylor Foundation's "BIO301 Unit 7 Quiz"
Link: The Saylor Foundation's "BIO301 Unit 7 Quiz" (PDF)

Instructions: Please complete the linked quiz to test your knowledge of the material covered in Unit 7. When you are done, check your work against The Saylor Foundation's "BIO301 Unit 7 Quiz Answer Key” (PDF).
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Unit 8: Meiosis

Meiosis, the other form of cell division, is the process by which one cell becomes four genetically unique cells. This process is essential to reproduction and the creation of unique offspring, which ultimately adds diversity to life. Meiosis is the reason you look similar to (but not exactly like) your parents. As in mitosis, meiosis is comprised of four phases. However, meiosis takes place in two stages, meiosis I and II. Most importantly, there is period of genetic recombination in meiosis during which the maternal and paternal DNA mix and result in the development of unique genomes. You should also note that, unlike mitosis, meiosis results in haploid cells and only takes place in two types of cells: sperm and oocyte cells.

Unit 8 Time Advisory show close

Unit 8 Learning Outcomes show close

Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Meiosis and Fertilization”
Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Meiosis and Fertilization” (HTML)

Instructions: Read the introduction and the subsection “Process of Meiosis,” along with all associated figures (Figs. 14.32-14.36). This will cover the topics outlined in subunits 8.1-8.3.

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Lecture: UC Berkeley: Professor David G. Drubin’s “Meiosis”
Link: UC Berkeley: Professor David G. Drubin’s “Meiosis” (YouTube)

Also available in:
iTunes U

Instructions: Scroll down the webpage to item 15 titled Lecture 28: “Meiosis,” and click on “View in iTunes.” Please watch this entire video lecture, which covers the topics outlined in subunits 8.1-8.3.

Terms of Use: The above video is reposted from the University of California – Berkeley’s Webcast.Berkeley. This video is released under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.
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8.1 Meiotic Prophase

Web Media: The Saylor Foundation’s “Figure 8.1”
Link: The Saylor Foundation’s “Figure 8.1” (PNG)

Instructions: Please open The Saylor Foundation’s Figure 8.1. Note that this subunit is covered by the reading and video assigned beneath Unit 8.
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8.1.1 Leptotene