# Saylor.org's Cell Biology
## Contents
### Review of Basic Concepts

Upon successful completion of this unit, students will be able to:
* Identify the functions of major organic molecules.
* Understand hydrophilic and hydrophobic bonds and their respective roles in cells (particularly in terms of cell-membrane structure).
* Understand the four levels of protein structures and be able to identify which structure is referred to in a given example.
* Understand the relationship between free energy and the direction of a reaction.
    1.1 Biology
       1.1.1 Amino Acids
       1.1.2 Four Levels of Protein Structures
       1.1.3 Carbohydrates
       1.1.4 ATP
       1.1.5 DNA and RNA
       1.1.6 Free Energy and ATP

### The Cell Membrane

Upon completion of this unit, students will be able to:
* Know and identify the components of membranes.
* Understand how these components affect membrane properties.
* Identify types of membrane transport (specific pumps and channels) and understand the role of various molecules and ions (e.g. sodium, calcium) in this transport.
    2.1 Membrane Components
       2.1.1 Lipids, Sphingolipids, Glycolipids
       2.1.2 Sterols
    2.2 Fluid Mosaic Model
    2.3 Membrane Pumps
       2.3.1 Glycophorin and Bacteriorhodopsin
       2.3.2 ATP-Driven Pumps
       2.3.3 ABC (ATP-Binding Cassette) Transporters
    2.4 Membrane Channels
       2.4.1 Sodium and Potassium Channels
       2.4.2 Leak Channels and Membrane Potential
       2.4.3 Water Channel
    2.5 Membrane Physiology
       2.5.1 Glucose Transport in Intestines
       2.5.2 Synthesis of ATP in Mitochondria

### Cell Signaling

Upon completion of this unit, students will be able to:
* Distinguish between different signaling pathways.
* Identify the function and roles of different kinds of receptors in the cell-signaling process.
* Understand the steps involved in signaling pathways and determine, when given certain conditions, what step of the process will be affected.
    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, Guanylyl Cyclase Receptors, and the 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 and Calcium
       3.4.3 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

### The Extracellular Matrix (ECM)

Upon completion of this unit, students will be able to:
* Answers questions about ECM molecules, including their functions and where each type of molecule is most common.
* Understand the functions of different kinds of adhesion molecules.
* Distinguish between types of intercellular junctions.
    4.1 ECM Molecules
       4.1.1 Collagen
       4.1.2 Elastic Fibers
       4.1.3 Proteoglycans, Glycosaminoglycans, and Hyaluronan
       4.1.4 Adhesive Glycoproteins
    4.2 Basal Lamina
    4.3 Cellular Adhesion Molecules (CAMs)
    4.4 Intercellular Junctions
       4.4.1 Tight Junctions
       4.4.2 Gap Junctions
       4.4.3 Adherens Junctions and Desmosomes
    4.5 ECM and Connective Tissue
       4.5.1 Loose Connective Tissue (LCT)
       4.5.2 Dense Connective Tissue (DCT)

### The Cytoskeleton

Upon completion of this unit, students will be able to:
* Understand the different roles of actin, tubulin, and intermediate filaments.
* Understand the properties and functions of actin, tubulin, and intermediate filaments.
* Understand the means through which cytoskeletal molecules are formed.
* Be able to determine which cytoskeletal molecule or process has been disrupted when given an example of a particular cellular problem or lack of function.
* Understand the relationship between cytoskeletal elements and cell/intracellular movements.
    5.1 Cytoskeleton Molecules
       5.1.1 Actin and Myosin
       5.1.2 Microtubules and Tubulin
       5.1.3 Intermediate Filaments
    5.2 Actin Family
       5.2.1 Actin Polymerization
       5.2.2 Actin Filament Cross-Linking (or “Bundling”) Proteins
    5.3 Tubulin
       5.3.1 Microtubule Assembly from GTP Tubulin
       5.3.2 Microtubule Associated Proteins
    5.4 Cytoskeletal Models
       5.4.1 Treadmilling
       5.4.2 Cell Crawling
       5.4.3 Desmosomes and Hemidesmosomes
       5.4.4 Skeletal Muscle Filament
       5.4.5 Kinesin-Dynein
       5.4.6 Cilia and Flagella

### The Cell Nucleus and Gene Expression

Upon completion of this unit, students will be able to:
* Distinguish between euchromatin and heterochromatin in terms of which is the active form of genes.
* Identify the components of the nuclear envelope and their functions.
* Understand the roles of enhancers and repressors in gene expression.
* Answer questions about gene regulation (pre- and post-transcription).
    6.1 Chromosome Organization/Chromatin
    6.2 Nuclear Organization
       6.2.1 Inner and Outer Membrane
       6.2.2 Nuclear Pore Complexes
       6.2.3 Transport across the nuclear envelope
       6.2.4 Nuclear Lamina
       6.2.5 Nucleolus
    6.3 Gene Expression Transcription Unit
       6.3.1 RNA Polymerases
       6.3.2 General Transcription Factors and DNA Binding Domains
       6.3.3 RNA Maturation
       6.3.4 Ribosome
       6.3.5 Translation
    6.4 Regulation of Gene Expression
       6.4.1 Chromatin Structure and DNA Methylation Regulates Trancription
       6.4.2 Repressors and Enhancers
       6.4.3 Inducible Systems

### Mitosis and Cytokinesis

Upon completion of this unit, students will be able to:
* Identify what major cellular events occur at each phase of the mitotic cell cycle and during cytokinesis.
* Distinguish between open and closed mitosis.
* Understand how to visually identify the phases of the mitotic cycle.
    7.1 Prophase
    7.2 Prometaphase
    7.3 Metaphase
    7.4 Anaphase
       7.4.1 Anaphase A
       7.4.2 Anaphase B
    7.5 Telophase
    7.6 Cytokinesis

### Meiosis

Upon completion of this unit, students will be able to:
* Identify what major cellular events occur at each phase of the meiotic cell cycle.
* Distinguish between mitosis and meiosis in terms of both specific cellular events and the types of cells resulting from the process.
* Understand the differences between oocyte formation and sperm formation.
    8.1 Meiosis I
    8.3 Meiosis II
    8.4 Regulation of Oocyte Meiosis

### The Cell Cycle

Upon completion of this unit, students will be able to:
* Understand what cellular events (or lack of events) occur during each phase of the cell cycle.
* Identify in what phase of the cycle specific types of cells are found.
* Understand the roles of cyclin and CDKs in regulating the cell cycle.
* Answer questions about the cyclin/CDK pathway and what molecules/intracellular events are involved in different aspects of cell-cycle regulation.
    9.1 General Phases of Cell Cycle
    9.2 Checkpoints of Cell Cycle
    9.3 Cyclins and Cyclin-Dependent Kinases (CDKs)
       9.3.1 Positive and Negative Regulators of CDK and Cyclin Pairs
       9.3.2 Cyclin Degradation

### Cellular Transport

Upon completion of this unit, students will be able to:
* Understand the roles of various organelles and molecules in cellular transport.
* Understand the roles of receptors in cellular transport.
* Answer questions about vesicular transport and the specific functions of different types of vesicles.
    10.1 Nuclear Transport
       10.1.1 Nuclear Import
       10.1.2 Nuclear Export
    10.2 Co-translational Targeting in the Nucleus
       10.2.1 Signal Recognition Particle (SRP), SRP Receptor, and Translocation
       10.2.3 N-Linked Glycosylation and Rough ER Processing
    10.3 Post-translational Targeting to Organelles
       10.3.1 Transport to Mitochondria
       10.3.2 Transport to Chloroplasts
    10.4 Vesicular Transport
       10.4.1 COP I (Coat Complex), COP II, Clathrin, and SNARES
       10.4.2 Dynamin and Caveolin Families

### Specialized Organelle Functions

Upon completion of this unit, students will be able to:
* Identify specialized organelles and their specific functions.
* Answer questions about where one would expect to find more of specific organelles (demonstrating an understanding of organelle function as it relates to larger tissue- and organ-wide processes).
* Recognize the similarities and differences between mitochondria and chloroplasts.
    11.1 Digestive Organelles
       11.1.1 Lysosomes
       11.1.2 Peroxisomes and Glyoxysomes
    11.2 Golgi
       11.2.1 Structure of the Golgi
       11.2.2 Glycosylation, lipid and polysaccharide metabolism
       11.2.3 Transport of Membrane Proteins
    11.3 Smooth ER
       11.3.1 Gluconeogenesis
       11.3.2 Detoxification and Cytochrome P450 Family
    11.4 Mitochondria
    11.5 Chloroplasts
       11.5.1 Carbon-Fixation
       11.5.2 Photosystem I and II