endomembrane system
Semi-autonomous organelles
Protein sorting to organelles
Systems biology of cells
Cell Biology & Cell Theory
Cell biology: The study of individual cells and their interactions.
Cell Theory (Schleiden & Schwann, with contributions from Virchow):
All living organisms are composed of one or more cells.
Cells are the smallest units of life.
New cells arise only from pre-existing cells through division (e.g., binary fission).
Origins of Life: Four Overlapping Stages
Stage 1: Formation of Organic Molecules
Primitive Earth conditions favored spontaneous organic molecule formation.
Hypotheses on the origin of organic molecules:
Reducing Atmosphere Hypothesis:
Earth's early atmosphere (rich in water vapor) facilitated molecule formation.
Stanley Miller’s experiment simulated early conditions, producing amino acids and sugars.
Extraterrestrial Hypothesis:
Organic carbon (amino acids, nucleic acid bases) may have come from meteorites.
Debate exists over survival after intense heating.
Deep-Sea Vent Hypothesis:
Molecules formed in the temperature gradient between hot vent water & cold ocean water.
Supported by experimental evidence.
Alkaline hydrothermal vents may have created pH gradients that allowed organic molecule formation.
Stage 2: Formation of Polymers
Early belief: Prebiotic synthesis of polymers was unlikely in aqueous solutions (water competes with polymerization).
Experimental evidence:
Clay surfaces facilitated the formation of nucleic acid polymers and polysaccharides.
Stage 3: Formation of Boundaries
Protobionts: Aggregates of prebiotically produced molecules enclosed by membranes.
Characteristics of a protobiont:
Boundary separating the internal & external environments.
Polymers with information (e.g., genetic material, metabolic instructions).
Catalytic functions (enzymatic activities).
Self-replication.
Liposomes:
Vesicles surrounded by lipid bilayers.
Can enclose RNA and divide.
Stage 4: RNA World Hypothesis
RNA was likely the first macromolecule in protobionts due to its ability to:
Store information.
Self-replicate.
Catalyze reactions (ribozymes).
Chemical Selection & Evolution:
RNA mutations allowed faster replication & self-sufficient nucleotide synthesis.
Eventually, RNA world was replaced by the DNA-RNA-protein world due to:
DNA providing more stable information storage.
Proteins offering greater catalytic efficiency and specialized functions.
Microscopy
Microscopy Parameters
Resolution: Ability to distinguish two adjacent objects.
Contrast: Difference between structures (enhanced by special dyes).
Magnification: Ratio of image size to actual size.
Types of Microscopes
Light Microscope: Uses light; resolution = 0.2 micrometers.
Electron Microscope: Uses electron beams; resolution = 2 nanometers (100x better than light microscopes).
Light Microscopy Subtypes
Bright Field: Standard; light passes directly through.
Phase Contrast: Amplifies differences in light phase shifts.
Differential Interference Contrast (DIC): Enhances contrast for internal structures.
Electron Microscopy Subtypes
Transmission Electron Microscopy (TEM):
Thin slices stained with heavy metals.
Some electrons scatter while others pass through to create an image.
Scanning Electron Microscopy (SEM):
Heavy metal-coated sample.
Electron beam scans the surface, producing 3D images.
Cell Structure & Function
Determined by matter, energy, organization, and information.
Genome: The complete set of genetic material.
Prokaryotic vs. Eukaryotic Cells
Feature Prokaryotic Cells Eukaryotic Cells
Nucleus ❌ Absent ✅ Present
Membrane-bound organelles ❌ None ✅ Yes
Size Small (1-10 µm) Large (10-100 µm)
Examples Bacteria, Archaea Plants, Animals, Fungi, Protists
Prokaryotic Cell Structure
Plasma Membrane: Lipid bilayer barrier.
Cytoplasm: Internal fluid.
Nucleoid Region: DNA storage (no nucleus).
Ribosomes: Protein synthesis.
Cell Wall: (Some) Provides structure & protection.
Glycocalyx: Protection & hydration.
Flagella: Movement.
Pili: Attachment.
Eukaryotic Cell Structure
Nucleus: Contains DNA & controls cell functions.
Organelles:
Rough ER: Protein synthesis & sorting.
Smooth ER: Lipid synthesis, detoxification.
Golgi Apparatus: Protein modification & sorting.
Mitochondria: ATP production (Powerhouse of the Cell™).
Lysosomes: Digestive enzymes for breakdown & recycling.
Peroxisomes: Breakdown of harmful substances.
Cytoskeleton: Provides structure (microtubules, actin filaments, intermediate filaments).
Plasma Membrane: Regulates transport & signaling.
Endomembrane System
Includes: Nucleus, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane.
Nuclear Envelope:
Double membrane structure.
Nuclear pores allow molecule transport.
Golgi Apparatus:
Modifies & sorts proteins/lipids.
Packages proteins into vesicles for secretion (exocytosis).
Lysosomes:
Contain acid hydrolases for macromolecule breakdown.
Perform autophagy (organelle recycling).
Semi-Autonomous Organelles
Mitochondria
Function: ATP production (cellular respiration).
Structure:
Outer & inner membrane (inner folds = cristae for increased surface area).
Mitochondrial matrix houses metabolic enzymes.
Chloroplasts (Plants & Algae)
Function: Photosynthesis (light energy → chemical energy).
Structure:
Outer & inner membrane.
Thylakoid membrane (site of photosynthesis).
Contains chlorophyll.
Endosymbiosis Theory
Mitochondria & chloroplasts evolved from free-living bacteria that were engulfed by an ancestral eukaryotic cell.
Protein Sorting & Cell Organization
Co-translational sorting:
Proteins destined for ER, Golgi, lysosomes, vacuoles, or secretion.
Post-translational sorting:
Proteins sent to nucleus, mitochondria, chloroplasts, peroxisomes.
Systems Biology
Studies how cellular components interact to form a functional system
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