This topic will explore the origins of the eukaryotic cell and explore briefly the behavior of cancer cells vs normal cells. Cell culture will also be covered.

1.1 Origins of Eukaryotic Cells: Life in the form of cells is introduced. Prokaryotic and Eukaryotic cells are introduced. Advantages of being multicellular are considered. Cell types are introduced as well as cell culture technology for in vitro analysis of cells. Cell culture technology is used to investigate how a cell walks.

● Origins of Eukaryotic Cells
● Examples of Single-Cell Eukaryotic Cells
● Multicell Eukaryotic Cells
● Cells from Organ Systems
● Cell Culture Technology: A Brief History
● How Cells Walk
● Five Steps of Directional Cell Walking
● Biomolecular Machines

1.2 Comparing Normal and Cancer Cells: This module examines phenomena reported from studies conducted using in vitro cell culture technology that distinguishes between normal cells and cancer cells, including step-wise changes that occur as the normal cell becomes a cancerous cell.

● Normal Cells: Anchorage-Dependency for Growth and Mortality
● Cancer Cells: Anchorage-Independent for Growth and Immortal
● Phases of the Cell Cycle—Noncancerous Cell
● Cell Cycle Phases—Cancerous Cell
● Transformation or Aneuploidy

1.3 The Technology of Making a Cell Line: A fundamental technology in Cell Biology is to make a cell line and to be able to grow these cells without contamination. This technology
has been seminal to basic research, to medicine, and to the development of pharmaceutical drugs (in clinical trials), to name a few areas.

● Basics of Making a Cell Line
● Primary Explants
● Primary Culture
● Secondary Culture
● Making a Cell Line
● Significance of Using a Cell Line

1.4 Cell Culture Incubator: This section covers the biological parameters that are needed to grow cell in vitro.

● Media and Aseptic Handling
● Change in Temperature of Human Cells
● Cell Culture Medium and their Purposes

1.5 Evolution of Eukaryotic Cells: The evolution of eukaryotic cells will be reviewed including the presumed evolution of the endomembrane system, mitochondria and chloroplasts. The importance of the ability of cells to locomote/move will also be reviewed.

● Eukaryotic Cells: Two Major Changes
● Comparison of Extant Prokaryotic and Eukaryotic Cells
● Loss of the Cell Wall
● Evolution of the Endomembrane System
● The Endosymbiotic Origin of Mitochondria and Chloroplasts
● The Ability to Locomote and the Cytoskeleton

This topic explores the outer boundary of the cell, the plasma membrane. The cell biology chemistry in this module starts at the outer edge of the cell and continues with points relevant to lipids and proteins that make up the membrane.

Module 2.1: Biological Membranes-Plasma Membrane Lipids: This module will introduce Biological Membranes with a focus on the lipid bilayer.

● The Building Blocks of the Cell and Plasma Membrane
● Biological Membranes and the Plasma Membrane
● Lipid Membranes
● Role of Cholesterol at High and Low Temperatures
● Cholesterol Protects the Lipid Bilayer from Freezing
● Chemical Structures of Phospholipids

2.2 Analyzing Lipids of Biological Membranes: How do we investigate the role of any one type of component in a biological membrane? Combined, there are hundreds to thousands of different types of proteins and lipids in a biological membrane; technology is required as the cell and its components are too small to be detected with human senses.

● Lipids in a Membrane
● Differential Scanning Calorimetry

2.3 Lipid Packing in Membranes: The biological membrane’s ability to partition water and compartmentalize enzymes depends on how tightly the lipids fit together in both of the lipid bilayers that make up the membrane. How tightly the lipids of the membrane pack together depends on the overall shape of the lipids.

● Structure of a Phospholipid
● Difference Between Phospholipids

2.4: Membrane Proteins: Proteins make up an important component of biological membranes. This section introduces characteristics of proteins that enable them to interact with biological membranes.

● Membrane Proteins
● The Structure of Membrane Proteins
● How Proteins Fold and Interact with One Another
● Long Chain of Amino Acids—Polar and Nonpolar
● Levels of Protein Structures

2.5 Transmembrane Proteins: This section examines transmembrane proteins as receptors and channels and their role in passive and active transport. Membrane anchors and the role they can play in subcellular localization/geography will be observed.

● What Do Transmembrane Proteins Do?
● The Shape of Transmembrane Proteins
● Channel Functions of TMPs
● TMPs: Passive and Active Transport
● Some Transmembrane Proteins Help Cells Walk
● Membrane Anchors Position as Special Class of Membrane-
Associated Proteins
● Gated Transport for a Transmembrane Protein
● Membrane Channels

This topic delves deeper into the cell and explores what lies between the plasma membrane and the nucleus. The focus is on the three cytoskeletal systems – what is on the surface and what is inside.

3.1 Actin Filaments: This section introduces three cytoskeletal filament systems: Actin filament, microtubules, and intermediate filament. These systems have numerous associated proteins that regulate and organize the network and are referred to as cytoskeletal systems since they are made of many proteins.

● Actin Monomers: Structure and Polarity
● Actin Filaments: Assembly/Disassembly
● Geography of Actin Filaments Within a Cell
● Organizing the Actin Filament Network
● How Does Myosin I Function as a Molecular Motor Protein?
● Myosin II: Structure
● Myosin II: A Technological Tool
● Actin Monomers—Structure and Polarity

3.2 Microtubules: This module introduces microtubules, one of the three cytoskeletal systems in the cell. The properties regulating this system will be described as well as its geographical significance within the cell.

● Microtubule: Structure and Polarity
● Microtubule Assembly/Disassembly
● Geography of Microtubules Within a Cell
● Specialized Microtubule-Based Structures
● Microtubule Network-Associated Proteins
● Visualization of Microtubular Polarity

3.3 Intermediate Filaments: Intermediate filaments with associated proteins are one of the three cytoskeletal systems present in eukaryotic cells. Intermediate filaments are different from the other two cytoskeletal systems (i.e.,the actin and microtubule systems), which will be explained in this module.

● Intermediate Filaments: Structure and Polarity
● Intermediate Filaments: Assembly
● Geography of Intermediate Filaments Within a Cell
● Nuclear Lamina
● Intermediate Filament-Associated Proteins
● Intermediate Filaments: The Strongest
● Resistance to Mechanical Stress
● Delayed Biochemical Confirmation?

3.4 Intercellular Junctions: Epithelial tissue has the unique role of extending the function of biological membranes over large sheets of cell (i.e., tissues). The special proteins causing this are discussed in this module.

● Epithelial Cells: Cells that Do Not Walk
● Tight Junctions: Creating a Physical Barrier
● Adhering/Anchoring Junctions; Strengthening Tight Junctions
● Lack of Communication
● Gap Junctions: Communicating Junctions
● The Anastomosing Layer—Tight Junction vs Adhering Junction

3.5 Cell Fractionation: In this module, we will compare the processes, tools, and chemicals involved in cell fractionation across two different methods: 1) a classic approach that separates the nuclear and cytoplasmic fraction and 2) an approach that separates the cell into cytoskeletal and soluble fractions.

● Nuclear and Cytoplasmic Fractionation
● Cytoskeletal and Soluble Fractionation
● Homogenization Buffer—Components, Purpose, and Temperature

This topic works from the nucleus back out to the surface using the Endomembrane System (co-translational insertion and membrane flow). How do the membrane components in membrane flow move via the cytoskeleton?

4.1 Endomembrane System: The endomembrane system is a unique feature of eukaryotic cells that has many functions. This section will introduce this membrane pipeline and focus on how a special population of mRNAs reach the endoplasmic reticulum as well as 3 resident proteins of the endoplasmic reticulum.

● Endomembrane System: An Evolutionary Advancement That Made Eukaryotic Cells
● Proteins Synthesized from Membrane-Bound Polyribosomes
● Co-Translational Insertion of Newly Synthesized Proteins
● First Steps of Co-Translational Insertion

4.2 Membrane/Protein Flow: The story of the endomembrane system and how proteins and lipids move and become targeted to specific locations in the cells continues. Once new lipids and new luminal and transmembrane proteins are part of the ER, the carbohydrate trees, proteins, and lipids undergo further changes in the ER.

● Endoplasmic Reticulum
● Membrane and Protein Flow
● How to Target Vesicles
● Functions of the SER

4.3 Golgi Apparatus and Exocytosis: The Golgi apparatus is the packaging center for proteins and lipids to be delivered to the rest of the cell.

● Golgi Apparatus: Processing Center for the Cell
● Constitutive and Regulative Exocytosis
● Inside-Outside Rule During Constitutive and Regulative Exocytosis

4.4 Making a Lysosome: Similar to the macro structures of the digestive system, lysosomes are responsible for the breakdown of molecules ingested by the cell into simple building blocks. Redistribution of these smaller building blocks by vesicular transport at the cell mirrors the function of the circulatory system.

● Enzymes in a Lysosome: A Potential Cell Atomic Bomb
● Lysosomal Enzymes
● Making a Lysosome

4.5 Protected Compartment of the Nucleus: The nucleus is a protected compartment. The nuclear envelope formed as the endomembrane system evolved; it surrounds the genetic information–the blueprints of life.

● Protective Features of the Nucleus
● Nuclear Pore Complex Pathway
● Signal Sequences for Entering the Nucleus
● How Histones Enter the Nucleus

4.6 Orphaned Organelles: The evolutionary origin of the mitochondria and chloroplasts began with one proto-prokaryotic organism engulfing another, but these are orphaned from the membrane flow system. Both have to acquire new lipids and proteins.

● The Endomembrane System: Evolution
● Orphaned Organelles: How Do They Get Lipids? How Do They Get New Proteins?
● Signal Sequence On a Nascent Protein
● Protein Signal Sequences
● Parts of Mitochondria

This topic explores cell communication, the equivalent of our internet communication. This connects every part of cell regulation and provides homeostatic feedback.

5.1: Endocytosis and Exocytosis: Another part of membrane flow is the cycle of endocytosis (taking in food) and exocytosis (removal of undigested food). This includes the recovery of receptors and lipids that have been accidentally placed in the plasma membrane.
● Endocytosis
● Phagocytosis, Pinocytosis, and Receptor-Mediated Endocytosis
● Exocytosis
● Transcytosis
● Clathrin-Dependent Endocytosis

5.2: Signal Transduction-Ligands and Receptors: The binding of ligands to receptors enable the cell to respond to stimuli from their environment. The resulting signal transduction cascades are responsible for life. This section covers the different types of signal transduction.

● Signal Transduction: A Dichotomy of Pathways
● Receiving/Responding to Environmental Stimuli by Means of Ligands and Receptors
● Communication Between Cells: How Do Cells Know They Have Received a Signal
● Signal Transduction Within Cells
● Ligand Binding to a Receptor

5.3 GTP-Binding Proteins: In this section, GTP binding proteins will be presented which require ligands binding to receptors. Then we will introduce the first of two major forms of cytoplasmic signaling, one acting through intracellular-free calcium where the signal can either be global or local.

● Understanding the Mechanisms of Signal Transduction
● GTP-Binding Proteins and Their Coupled Receptors
● Intracellular-Free Calcium in Cytoplasmic Signal Transduction
● Starting and Stopping a Calcium Signal Types of GTP-BindingProtein

5.4 Kinases in Cytoplasmic Signal Transduction: Signal transduction events triggered by cell-cell communication can result in cytoplasmic signaling through kinase activity. The ratio of cytoplasmic signals at each point in the cell can give a unique chemical status to that point, and is another way to evaluate the geography of the cell.

● Conformational Change of Protein Shape by Kinase and Phosphatase Activity
● Kinases in Eukaryotic Cells
● Global and Local Kinase Signals
● XYZ Coordinates for Each Point In the Cell
● Conformational Change of Protein Shape by Kinase and Phosphatase Activity

5.5 Cytoplasmic Signal Transduction: Four important cytoplasmic signal transduction pathways will be examined in some detail. These four pathways employ different types of geography (i.e., subcellular localization).

● Stress Cable Assembly and Contraction
● Calmodulin: An Accelerator for Calcium Signaling
● Protein Kinase A (PKA)
● Calcium/Calmodulin Dependent Protein Kinase II (CaM Kinase II)
● Protein Kinase C (PKC)
● Tyrosine Kinase: The Insulin Receptor
● The MAP Kinase Pathway
● Importance of Calcium in Bipolar Fiber
● Sequence of the PKC Pathway

This topic explores the cell cycle and cell division. How do all the parts of the cell and their behavior act in concert to renew life, developing from one cell into two?

6.1 Cell Cycle: Signal transduction regulates the cell cycle through cyclin-dependent kinases (CDKs) activated by the binding of cyclin. Pairings of different CDKs and cyclins regulate checkpoints at pivotal sites in the cell cycle. One of these regulates M-Phase where DNA condenses into chromosomes.

● Phases of the Cell Cycle
● Regulation of the Cell Cycle by Cytoplasmic Signal Transduction
● Function of APC/C

6.2 Karyokinesis and Cytokinesis: Historically, technological limitations caused a focus on the 1 hour of M-phase in cells as it was unclear what was happening in interphase. Mitosis has three major phases: 1) separating the chromosome, 2) settling down the cytoplasm, and 3) separating the cytoplasm of a single cell into two-cell cytokinesis.

● Brief History of Studies on Mitosis
● Phases of Karyokinesis
● Cytokinesis
● Stages of Mitosis and Cytokinesis