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JoVE Core: Cell Biology

JoVE Core: Cell Biology illustrates complex cellular processes in easy-to-understand yet comprehensive animated video lessons. This collection focuses on the essential components and functions of cells, including organelles and membranes, cellular transport, and cell energetics.

Chapter 1: Cells, Genomes, and Evolution

  • What are Cells?
  • The Tree of Life - Bacteria, Archaea, and Eukaryotes
  • Prokaryotic Cells
  • Eukaryotic Compartmentalization
  • Eukaryotic Evolution
  • Animal and Plant Cell Structure
  • Cytoplasm
  • The Nucleus
  • The DNA Helix
  • The Central Dogma
  • Mutations
  • Genome Size and the Evolution of New Genes
  • Gene Families
  • Gene Evolution - Fast or Slow?
  • Types of Genetic Transfer Between Organisms

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Chapter 2: Biochemistry of the Cell

  • The Periodic Table and Organismal Elements
  • Functional Groups
  • Types of Chemical Bonds
  • Noncovalent Attractions in Biomolecules
  • Polymers
  • What are Lipids?
  • Structure of Lipids
  • Chemistry of Carbohydrates
  • Nucleic Acids
  • Protein and Protein Structures
  • pH Regulation in Cells
  • Chemistry of Life

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Chapter 3: Energy and Catalysis

  • First Law of Thermodynamics
  • Second Law of Thermodynamics
  • Enthalpy within the Cell
  • Entropy within the Cell
  • Introduction to Free Energy
  • Endergonic and Exergonic Reactions in the Cell
  • The Equilibrium Binding Constant and Binding Strength
  • Free Energy and Equilibrium
  • Non-equilibrium in the Cell
  • Oxidation and Reduction of Organic Molecules
  • Introduction to Enzymes
  • Enzymes and Activation Energy
  • Introduction to Enzyme Kinetics
  • Turnover Number and Catalytic Efficiency
  • Catalytically Perfect Enzymes
  • Introduction to Mechanisms of Enzyme Catalysis
  • Ligand Binding and Linkage
  • Cooperative Allosteric Transitions
  • Ribozymes
  • ATP Energy Storage and Release
  • ATP and Macromolecule Synthesis
  • Coupled Reactions

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Chapter 4: Introduction to Metabolism

  • Overview of Metabolism
  • Carbohydrate Metabolism
  • Glycolysis: Preparatory Phase
  • Glycolysis: Pay-off Phase
  • Fates of Pyruvate
  • Role of Reduced Coenzymes NADH and FADH2
  • Overview of Nitrogen Metabolism
  • Overview of Fatty acid Metabolism
  • Sugars as Energy storage Molecules
  • Fats as energy storage Molecules
  • Regulation of Metabolism
  • Metabolic Feedback Loops

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Chapter 5: Protein Structure

  • What are Proteins?
  • Protein Organization
  • Protein Folding
  • Protein Families
  • Conservation of Protein Domains Over Different Proteins
  • Globular and Fibrous Proteins
  • Intrinsically Disordered Proteins
  • Protein Complex Assembly
  • Conjugated Proteins
  • Amyloid Fibrils

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Chapter 6: Protein Function

  • Ligand Binding Sites
  • Protein-protein Interfaces
  • Conserved Binding Sites
  • Cofactors and Coenzymes
  • Cooperative Allosteric Transitions
  • Protein kinases and Phosphatases
  • GTPases and their Regulation
  • Covalently Linked Protein Regulators
  • Protein Complexes with Interchangeable Parts
  • Mechanical Protein Functions
  • Structural Protein Functions
  • Protein Networks

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Chapter 7: Structure and Organization of DNA

  • DNA as a Genetic Template
  • Structure of a Gene
  • Chromosome Structure
  • The Nucleosome
  • Chromatin Packaging
  • Euchromatin
  • Heterochromatin
  • Histone Modification
  • Lampbrush Chromosomes
  • Polytene Chromosomes

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Chapter 8: DNA Replication and Repair

  • Base-pairing and DNA Repair
  • The DNA Replication Fork
  • Lagging Strand Synthesis
  • The Replisome
  • Proofreading
  • Replication in Prokaryotes
  • Replication in Eukaryotes
  • Telomeres and Telomerase
  • Overview of DNA Repair
  • Base Excision Repair
  • Nucleotide Excision Repair
  • Mismatch Repair
  • Fixing Double-strand Breaks
  • Homologous Recombination
  • Gene Conversion
  • DNA Damage can Stall the Cell Cycle
  • Restarting Stalled Replication Forks

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Chapter 9: Transcription: DNA to RNA

  • What is Gene Expression?
  • RNA Structure
  • Types of RNA
  • Transcription
  • Bacterial RNA Polymerase
  • Eukaryotic RNA Polymerases
  • General Transcription Factors
  • RNA Polymerase II Accessory Proteins
  • Transcription Elongation Factors
  • Pre-mRNA Processing: Modification of pre-mRNA Ends
  • RNA Splicing
  • Chromatin Structure and RNA Splicing
  • Alternative RNA Splicing
  • Nuclear Export of mRNA
  • Transfer RNA Synthesis
  • Ribosomal RNA Synthesis
  • The Nucleolus
  • Additional Subnuclear Structures

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Chapter 10: Translation: RNA to Protein

  • Translation
  • Ribosomes
  • tRNA Activation
  • Initiation of Translation
  • Termination of Translation
  • Improving Translational Accuracy
  • Nonsense-mediated mRNA Decay
  • Molecular Chaperones and Protein Folding
  • The Proteasome
  • Regulated Protein Degradation
  • Proteins: From Genes to Degradation

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Chapter 11: Control of Gene Expression

  • Cell Specific Gene Expression
  • Regulation of Expression Occurs at Multiple Steps
  • Cis-regulatory Sequences
  • Cooperative Binding of Transcription Regulators
  • Prokaryotic Transcriptional Activators and Repressors
  • The Eukaryotic Promoter Region
  • Co-activators and Co-repressors
  • Master Transcription Regulators
  • Regulated mRNA Transport
  • mRNA Stability and Gene Expression
  • MicroRNAs
  • siRNA - Small interfering RNAs
  • lncRNA - Long Non-coding RNAs
  • Epigenetic Regulation

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Chapter 12: Membrane Structure and Components

  • What are Membranes?
  • Membrane Fluidity
  • Fluid Mosaic Model
  • Membrane Lipids
  • Asymmetric lipid bilayer
  • Membrane Asymmetry Regulating Transporters
  • Membrane Carbohydrates
  • Membrane Proteins
  • Lipids as Anchors
  • Single-pass Transmembrane Proteins
  • Multi-pass Transmembrane Proteins and β-barrels
  • Detergent Purification of Membrane Proteins
  • Protein Diffusion in the Membrane
  • Membrane Domains
  • Mechanisms of Membrane Domain Formation
  • Mechanisms of Membrane-bending

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Chapter 13: Membrane Transport and Active Transport

  • The Significance of Membrane Transport
  • Membrane Transporters
  • Facilitated Transport
  • Primary Active Transport
  • ATP Driven Pumps I: Overview
  • ATP Driven Pumps II: P-type Pumps
  • ATP Driven Pumps III: V-type pumps
  • ABC Transporters: Exporter
  • ABC Transporters: Importer
  • Glucose Transporter
  • Secondary Active Transport
  • Transcellular Transport of Solutes
  • Glucose Absorption into the Small Intestine
  • Stomach pH regulation

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Chapter 14: Channels and the Electrical Properties of Membranes

  • Aquaporins
  • Non-gated Ion channels
  • Ligand-gated Ion Channels
  • Voltage-gated Ion Channels
  • Mechanically-gated Ion Channels
  • Neuron Structure
  • Resting Membrane Potential
  • Resting Potential Decay
  • Action Potential
  • Channelrhodopsins
  • Patch Clamp Technique
  • Electrical Synapses
  • Chemical Synapses
  • Excitatory and Inhibitory Effects of Neurotransmitters
  • Muscle Contraction
  • The Role of Ion Channels in Neuronal Computation
  • Long-term Potentiation
  • Long-term Depression

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Chapter 15: Transmembrane Transport in Endoplasmic Reticulum and Peroxisomes

  • The Endoplasmic Reticulum
  • Smooth Endoplasmic Reticulum - SER
  • Role of ER in the Secretory Pathway
  • Directing Proteins to the Rough Endoplasmic Reticulum (RER)
  • Protein Translocation Machinery on the ER Membrane
  • Cotranslational Protein Translocation
  • Post-translational Translocation of Proteins to the RER
  • Insertion of Single-pass Transmembrane Proteins in the RER
  • Multi-pass Transmembrane Proteins in the RER
  • Tail-anchoring Membrane Proteins in the ER
  • GPI Anchoring of Proteins in the ER Membrane
  • Protein Modifications in the RER
  • Protein Folding Quality Check in RER
  • Export of Misfolded Proteins Out of the ER
  • The Unfolded Protein Response
  • Regulation of the Unfolded Protein Response
  • Synthesis of Phosphatidylcholine in the ER Membrane
  • Assembly of the Lipid Bilayer in the ER
  • Peroxisomes
  • Protein Import into the Peroxisomes

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Chapter 16: Intracellular Compartments and Protein Sorting

  • Overview of Protein Sorting and Transport
  • Signal Sequences and Sorting Receptors
  • Nuclear Protein Sorting
  • Nuclear Localization Signals and Import
  • Nuclear Export
  • Directionality of Nuclear Transport
  • Regulation of Nuclear Protein Sorting
  • Mitochondrial Protein Sorting
  • Mitochondrial Precursor Proteins
  • Translocation of Proteins into the Mitochondria
  • Energy to Drive Translocation
  • Structure of Porins
  • Porin Insertion in the Outer Mitochondrial Membrane
  • Protein Transport into the Inner Mitochondrial Membrane
  • Protein Transport to the Thylakoids
  • Protein Transport to the Stroma
  • Protein Transport to the Outer Chloroplast Membrane
  • Protein Transport to the Inner Chloroplast Membrane

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Chapter 17: Intracellular Membrane Traffic

  • Introduction to Membrane Traffic
  • COP Coated Vesicles
  • Clathrin Coated Vesicles
  • Phosphoinositides and PIPs
  • Coat Assembly and GTPases
  • Pinching-off of Coated Vesicles
  • Rab Proteins
  • Rab Cascades
  • SNAREs and Membrane Fusion
  • Vesicular Tubular Clusters
  • ER Retrieval Pathway
  • Golgi Apparatus
  • Protein Glycosylation
  • Proteoglycans
  • Oligosaccharide Assembly
  • Golgi Matrix Proteins
  • Transport Across the Golgi
  • Lysosomes
  • Delivery Pathways to the Lysosome
  • Autophagy
  • Lysosomal Hydrolases

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Chapter 18: Endocytosis and Exocytosis

  • Endocytosis
  • Phagocytosis
  • Pinocytosis
  • Receptor-mediated Endocytosis
  • The Early Endosome: Endocytosis of Transferrin
  • Maturation of Endosomes
  • Intralumenal Vesicles and Multivesicular Bodies
  • Receptor downregulation in MVBs
  • Overview of Exosomes
  • Recycling Endosomes and Transcytosis
  • Transcytosis of IgG
  • Exocytosis
  • Overview of Secretory Vesicles
  • Insulin Secretory Vesicles
  • The Fusion of Secretory Vesicles with the Plasma Membrane
  • Enlargement of The Plasma Membrane
  • Synaptic Signaling

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Chapter 19: Mitochondria and Energy Production

  • Mitochondria
  • Mitochondrial Membranes
  • The Inner Mitochondrial Membrane
  • The Citric Acid Cycle: Overview
  • The Citric Acid Cycle: Output
  • Electron Transport Chain: Complex I and II
  • Electron Transport Chain: Complex III and IV
  • ATP Synthase: Mechanism
  • The Electron Transport Chain
  • The Supercomplexes in the Crista Membrane
  • ATP Synthase: Structure
  • The ADP/ATP Carrier Protein

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Chapter 20: Chloroplasts and Photosynthesis

  • What is Photosynthesis?
  • The Anatomy of Chloroplasts
  • The Calvin Benson Cycle
  • The Photochemical Reaction Center
  • The Antenna Complex
  • Photosystems
  • The Z-Scheme of Electron Transport in Photosynthesis

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