Cell Biology (As a Speciality only)
Cell Biology consists of scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move, grow, and reproduce. Finally, all organisms are able to regulate their own internal environments.
Cell Biologists are able to study life at multiple levels of organization, from biochemistry/molecular biology of a cell to the level of anatomy and physiology of plants and animals, and evolution of populations. Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use. Biologists study and classify the various forms of life, from prokaryotic organisms such as archaea and bacteria to eukaryotic organisms such as protists, fungi, plants, and animals. These various organisms contribute to the biodiversity of an ecosystem, where they play specialized roles in the cycling of nutrients and energy through their biophysical environment.
Topics /Lesson Coverage – CELL BIOLOGY
· Introducing to Cell Biology
o The Discovery of Cells
o Basic Properties of Cells
o Cells are Highly complex and Organised
o Cells Possess a Generic Program and the Means to Use It
o Cells Are Capable fo Producing More of Themselves
o Cell Acquire and Utilize Energy
o Cells Carry Out a Variety of Chemical Reactions
o Cells Engage in Mechanical Activities
o Cells are Able to Respond to Stimuli
o Cells are Capable of Self-Regulation
o Cells Evolve
o Two Fundamentally Different Classes of Cells
o Characteristics that Distinguish Prokaryotic and Eukaryotic Cells
o Types of Prokaryotic Cells
o Types of Eukaryotic Cells: Cell Specialization
o The Size of Cells and Their Components
o Synthetic Biology
• The Human Perspective: The Prospect of Cells Replacement Therapy.
o Viruses
o Viroid
· Experimental Pathways: The origin of Eukaryotic Cells.
· The Structure and Functions of Biological Molecules
o Covalent Bonds
· Polar and Non polar Molecules
· Ionization
o Noncovalent Bonds
• The Human Perspective: Free Radical as a Cause of Aging
o Ionic Bonds:Attractions between Charged Atoms
o Hydrogen Bonds
o Hydrophobic Interaction and van der Wals forces
o The Life supporting Properties of Water
o Acids, Bases, and Buffer
o The Nature of Biological Molecules
o Functional Group
o A Classification of Biological Molecules by Function
o Four types of Biological Molecules
o Carbohydrate
o Lipids
o Proteins
· The Human Perspective:Protein Misfolding can have deadly consequences
o Nucleic Acids
o The Formation of Complex Macromolecular Structures
o The Assembly of Tobacco Mosaic Virus Particles and Ribosomal Subunit
· Experimental Pathways: Chaperones: Helping Proteins Reach Their Proper Folded state.
· Bioenergetics, Enzymes, and Metabolism
o Bioenergetics
o The Laws of Thermodynamics and the Concept of Entropy Free Energy
o Enzymes as Biological Catalysts
o The Properties of Enzymes
o Overcoming the Activation Energy Barrier
o The Active Site
o Mechanisms of Enzyme Catalysis
o Enzyme Kinetics
· The Human Perspective: The Growing Problem of Antibiotic Resistance
o Metabolism
o An Overview of Metabolism
o Oxidation and Reducing: aMater of Electrons
o The Capture and Utilization of Energy
o Metabolic Regulation
· Genes, Chromosomes, and Genomes
o The Concept of a Gene as a Unit of Inheritance
o Chromosomes: The Physical Carriers of Genes
o The Discovery of Chromosomes
o Chromosome s the Carrier of Genetic Information
o Genetic Analysis in Drosophila
o Crossing over and Recombination
o Mutagenesis and Giant Chromosomes
o The Chemical Nature of the Gene
o The Structure of DNA
o The Watson-Crick Proposal
o DNA Supercoiling
o The Structure of the Genome
o The Complexity of the Genome
· The Human Perspective: Diseases that Result from Expansion of Trinucleotide Repeats
o The Stability of the Genome
o Whole – Genome Duplication (Polyploidization)
o Duplication and Modification of DNA Sequences
o “Jumping Genes” and the Dynamic Nature of the Genome
o Sequencing Genomes: The Footprints of Biological Evolution
o Comparative Genomics: “if it’s Conserved, it must be Important”.
o The Genetic Basis of “Being Human”
o Genetic Variation Within the Human Species Population
· The Human Perspective: Application of Genomic Analyses to Medicine.
· Experimental Pathway: The Chemical Nature of the Gene.
· The Path to Gene Expression
o The Relationship Between Genes, Proteins, and RNAs
o An Overview of the Flow of Information through the Cells
o An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells
o Transcription in bacteria
o Transcription and RNA Processing n Eukaryotic Cells
o Synthesis and processing and Processing of Eukaryotic Ribosomal and Transfer RNAs
o Synthesizing the rRNA Precursor
o Processing the rRNA Precursor
o Synthesis and Processing of the 5S rRNA
o Transfer RNAs
o Synthesis and Processing of Eukaryotic Messenger RNAs
o The Machinery for mRNA Transcription
o Split Genes: And Unexpected Finding
o The Processing of Eukaryotic of Split Genes and RNA Splicing
o Creating New Ribozymes in the Laboratory
o Smalls Regulatory RNSs and RNA silencing Pathways
• The Human Perspective:Clinical Applications or RNA Interference
o Micro RNAs: Small RNAs That Regulate Gene Expression
o siRNAs: A Class of Small RNAs that Function in Germ Cells
o Other Noncoding RNAs
o Encoding Genetic Information
o The Properties of the Genetic Code
o Decoding the Codons: The Role of Transfer RNAs
o The Structure of tRNAs
o Translating Genetic Information
o Initiation
o Elongation
o Termination
o mRNA surveillance and Quality Control Polyribosomes
· Experimental Pathways: The Role of RNA as a Catalyst
· Controlling Gene Expression
o Control of Gene Expression in Bacteria
o Organization of Bacterial Genomes
o The Bacterial Operon
o Riboswitches
o Control of Gene Expression in Eukaryotes: Structure and Function of the Cell’s Nucleus
o The Nuclear Envelope
o Chromosomes and Chromatin
· The Human Perspective: Chromosomal Aberrations and human Disorders
o Epigenetics: There’s More to Inheritance than DNA
o The Nucleus as a Organized Organelle
o An Overview of Gene Regulating in Eukaryotes
o Transcriptional Control
o The Role of Transcription Factors in Regulating Gene Expression
o The Structure of Transcription Factor
o DNA sites Involved in Regulating Transcription
o Transcriptional Activation: The Role of Enhancers, Promotes and Coactivators
o Transcriptional Repression
o RNA Processing Control
o Translational Control
o Initiation of Translation
o Cytoplasmic Localization of mRNAs
o The Control of mRNA Stability
o The Role of Micro RNAs in Translational Control
o Posttranslational Control: Determining Protein Stability
· Replicating and Repairing DNA
o DNA Replication
o Semiconserved Replication
o Replication in Bacterial Cells
o The Structure and Functions of DNA Polymerases
o Replication in Eukaryotic Cells
o DNA Repair
o Nucleotide Excision Repair
o Base Excision Repair
o Mismatch Repair
o Double-Stand Breakage Repair
o Between Replication and Repair
· The Human Perspective: The Consequences of DNA Repair Deficiencies
· Cellular Membranes
o An Overview of Membrane Functions
o A Brief History of Studies on Plasma Membrane Structure
o The Chemical Composition of Membranes
o Membrane Lipids
o The Asymmetry of Membrane Lipids
o Membrane Carbohydrates
o The Structure and Functions of Membrane Proteins
o Integral Membrane Protein
o Studying the Structure and Properties of Integral Membrane Proteins
o Peripheral Membrane Proteins
o Membrane Lipids and Membrane Fluidity
o The Importance of Membrane Fluidity
o Maintaining Membrane Fluidity
o Lapid Rafts
o The Dynamic Nature of the Plasma Membrane
o The Diffusion of Membrane Proteins After Cells Fusion
o Restrictions of Protein and Lipid Mobility
o The Red Blood Cell: An Example of Plasma Membrane Structure.
o The Movement of Substances Across Cell membranes
o The Energetics of Solute Movement
o Diffusion of Substances through Membranes.
o Facilitated Diffusion
o Active Transport
· The Human Perspective: Defects in Ion Disease the Transporters as a Cause of Inherited Disease
o Membrane Potentials and Nerve Impulses
o The Resting Potential
o The Action Potential
o Proagatioc of Action Potentials and Impulse
o Neurotransmission: Jumping the Symaptic Cleft
· Experimental Pathways: The Acetylcholine Receptor
· Mitochondrial Structure and Function
o Mitochondrial Structure and Function
o Mitochondrial Membranes
o The Mitochondrial Matrix
o Oxidative Metabolism in the Mitochondria
o The Tricarboxylic Acid (TCA) Cycle
o The Importance of Reduced Coenzymes in the Formation of ATP
· The Human Perspective: The Role of Anaerobic and Aerobic Metabolism in Exercises
o The Role of Mitochondria in the Formation of ATP
o Oxidation-Reduction Potentials
o Electron Transport
o Types of Electron Carrier
o Translocation of Protons and the Establishment of a Proton-Motive Force
o The Machinery for ATP Formation
o The Structure of ATP Synthase
o The Basis of ATP Formation According to the Binding
o Change Mechanism
o Other Roles for the Proton-Motive Force in Addition to ATP Synthesis
o Peroxisome
· The Human Perspective: Diseases that result from abnormal Mitochondrial or Peroxisomal Function
· Chloroplast Structure and Function
o Chloroplast Structure and Function
o An Overview of Photosynthetic Metabolism
o The Absorption of Light
o Photosynthetic Pigments
o Photosynthetic Units and Reaction Centres
o Oxygen Formation: Coordinating the Action of Two DifferentPhotosynthetic Systems
o Killing Weeds by Inhibiting Electron Transport
o Photophosphorylation
o Noncyclic Versus Cyclic Photophosphorylation
o Carbon Dioxide Fixation and the Synthesis of Carbohydrate
o Carbohydrate Synthesis in C3 Plant
o Carbohydrate Synthesis in C4 Plant
o Carbohydrate Synthesis in CAM Plant
· The Extracellular Matrix and Cell Interactions
o The Extracellular Space
o The Extracellular Matrix
o Interactions of Cells with Extracellular Materials
o Integrins
o Focal Adhesion and Hemidesmosomes: Anchoring Cells to Their Substratum
o Interactions of Cells with Other Cells
o Selectins
o The Immunoglobulin Superfamily
o Cadherins
· The Human Perspective: The Role of Cell Adhesion in Inflammation and Metastasis
o Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells
o The Role of Cell-Adhesion Receptors in Transmembrane Signalling
o Tight Junctions: Sealing the Extracellular Space
o Gap Junctions and Plasmodesmata: Mediating Intercellular Communication
o Plasmodesmata
o Cell Walls
· Cellular Organelles and Membrane Trafficking
o An Overview of the Endomembrane System
o A Few approaches to the Study of Endomembrane
o Insights Gained from Autoradiography
o Insight Gained from the Use of the Green Fluorescent Protein
o Insight Gained from the Biochemical analysis of Subcellular Fractions
o Insights Gained from the Use of Cell-Free Systems
o Insights Gained from the Study of Mutant Phenotypes
o The Endoplasmic Reticulum
o The Smooth Endoplasmic Reticulum
o Functions of the Rough Endoplasmic Reticulum
o From the ER to the Golgi Complex: The First Step in Vesicular Transport
o The Golgi Complex
o Glycosylation in the Golgi Complex
o The Movement of Materials through the Golgi Complex
o Types of Vesicle Transport and Their Functions
o COPII- Coated Vesicles: Transporting Cargo from the ER or the Golgi Complex
o COPI-Coated Vesicles: Transporting Escaped Process to the ER
o Beyond the Golgi Complex: Sorting Proteins at the TGN
o Targeting Vesicles to a particular Compartment
o Lysosomes
o Autophagy
· The Human Perspective: Disorders resulting from Defects in Lysosomal Function
o Plant Cells Vacuoles
o The Endocytic Pathway: Moving Membrane and Materials into the cell interior
o Endocytosis
o Phagocytosis
o Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplast
o Uptake of Proteins into Peroxisomes
o Uptake of Proteins into Mitochondria
o Uptake of Proteins into Chloroplasts
· Experimental Pathways: Receptor-Madate Endocytosis
· The Cytoskeleton
o Overview of the Major Functions of the Cytoskeleton
o The study of the Cytoskeleton
o The se of Live-Cell Fluorescence Imaging
o The Use of In Vitro and In Vivo Single-Molecule Assays
o The Use of Fluorescence Imaging Technique to Monitor the Dynamic of the Cytoskeleton
o Microtubules
o Structure and Composition
o Microtubule-Associated Proteins
o Microtubules as Structural Spots and Organizers
o Microtubules as Agents of Intracellular Motility
o Motor Proteins that Traverse the Microtubular Cytoskeleton
o Microtubule-Organizing Centres (MTOCs)
o The Dynamic Properties of Microtubules
o Cilla and Flagella: Structure and Function
· The Human Perspective: The Role of Cilla in Development and Disease
o Intermediate Filaments
o Intermediate Filament Assembly and Disassembly
o Types and Functions of Intermediate Filaments
o Microfilaments
o Microfilament Assembly and Disassembly
o Myosin: The Molecular Motor of Action Filaments
o Muscle Contractility
o The Sliding Filament Model of Muscle Contraction
o Non-muscle Motility
o Action-binding Proteins
o Example of Non-muscle Motility and Contractility
· Cell Division
o The Cell Cyle
o Cell Cycles in Vivo
o Control of the Cell Cycle
o M Phase: Mitosis and Cytokinesis
o Prophase
o Prometaphase
o Metaphase
o Anaphase
o Telophase
o Motor Proteins Required Mitotic Movements Cytokinesis
o Meiosis
o The Stage of Meiosis
· The Human Perspective: Meiotic Nondisjunction and Its consequences
o Genetic Recombination During Meiosis
· Experimental Pathways: The Discovery and Characterization of MPF
· Cell Signalling Pathways
o The Basic Elements of Cell Signalling Systems
o A Survey of Extracellular Messengers and Their Receptors
o G Protein-Couples Receptors and Their Second Messengers
o Signal Transduction by G Protien-Coupled Receptors
· The Human Perspective: Disorders Associated with G Protein-Coupled Receptors
o Second Messengers
o Teh Specificity of G Protein-Couple Responses
o Regulation of Blood Glucose Levels
o The Role of GPCRs in Sensory Perception
o Protein-Tyrosine Phosphorylation as a Mechanism of Signal Transduction
o Teh Ras-MAP Inase Pathway
o Signalling by the Insulin Receptor
· The Human Perspective: Signalling Pathways and Human Longevity
o Signalling Pathways in Plants
o The Role of Calcium as an Intracellular Messenger
o Regulating Calcium Concentrations in Plant Cells
o Convergence, Divergence, and Cross-Talk Among Different Signalling Pathways
o Example of Convergence, Divergence, and Cross – Talk Among Signalling Pathways
o The Role of NO as an Intercellular Messenger
o Apoptosis (Programmed Cell Death)
o The Extrinsic Pathway of Apoptosis
o The Intrinsic Pathway of Apoptosis
· Cancer
o Basic Properties of a Cancer Cell
o The Cause of Cancer
o The Genetics of Cancer
o Tumour-Suppressor Genes and Oncogenes: Brakes and Accelerators
o The Cancer Genome
o Gene-Expression Analysis
o New Strategies for combating Cancer
o Immunotherapy
o Inhibiting the Activity of Cancer-Promoting Proteins
o Inhibiting the Formation of New Blood Vessels (Angiogenesis)
· Experimental Pathways: The Discovery of Oncogenes
· Immunity
o An Overview of the Immune Response
o Innate Immune Reponses
o Adaptive Immune Responses
o The Clonal Selection Theory as It applies to B Cells
o Vaccination
o T Lymphocytes: Activation and Mechanism of Action
o Selected Topics on the Cellular and Molecular Basis of Immunity
o The MolecularStructure of Antibodies
o DNA Rearrangements that Produce Genes Encoding B-and T-Cell Antigen Receptors
o Membrane-Bound Antigen Receptor complexes
o Teh Major Histocompatibility Complex
o Distinguishing Self Nonself
o Lymphocytes Are Activated by Cell Surface by Signals
o Signal Transduction pathways in Lymphocyte Activation
· The Human Perspective: Autoimmune Diseases
· ExperimentalPathways: The Role of the Major Histocompatibility Complex in Antigen Presentation
· Methods in Cell Biology
o The Light Microscope
o Resolution
o Visibility
o Preparation of Speciments for Bright-Field Light Microscopy
o Phase-Contrast Microscopy
o Fluorescence Microscopy (and Related Fluorescence-Based Techniques)
o Video Microscopy and Image Processing
o Laser Scanning Confocal Microscopy
o Super-Resolution Fluorescence Microscopy
o Transmission electron Microscopy
o Specimen Preparation for Electron Microscopy
o Scanning Electron and Atomic Force Microscopy
o Atomic Force Microscopy
o The Use of Radioisotopes
o Cell Culture
o The Fraction of a Cell’s Contents by Differential Centrifugation
o Isolation, Purification, and Fractionation of Proteins
o Selective Precipitation
o Liquid Column Chromatography
o Polyacrylamide Gel electrophoresis
o Protein Measurement and Analysis
o Determining the Structure of Proteins and Multi-subunit Complexes
o Fractionation of Nucleic Acids
o Separation of DNAs by Gel Electrophoresis
o Separation of Nucleic Acids by Ultracentrifugation
o Nucleic Acid Hybridization
o Chemical Synthesis of DNA
o Recombinant DNA technology
• Restriction Endonucleases
• Formation of Recombinant DNAs
• DNA Cloning
o Enzymatic Amplification of DNA by PCR
• Applications of PCR
o DNA Sequencing
o DNA Libraries
• Genomic Libraries
• cDNA Libraries
o DNA Transfer into Eukaryotic Cells and Mammalian Embryos
o Determining Eukaryotic Gene Functions by Gene Elimination of Silencing
• In Vitro Mutagenesis
• Knockout Mice
• RNA Interference
o The Use of Antibodies