Chapter 04 Evolutionary Origin of Cells - Vocabulary Flashcards

Origin of Living Cells on Earth

Four overlapping stages to origin of life on Earth
- Stage 1: Nucleotides and amino acids were produced before cells existed
- Stage 2: Polymers (DNA, RNA, proteins) formed from nucleotides and amino acids
- Stage 3: Polymers enclosed by membranes to form boundary-containing structures
- Stage 4: Polymers enclosed by membranes acquired cellular properties
Stage 1: Origin of organic molecules
- Primitive Earth conditions may have favored spontaneous formation of organic molecules
- Prebiotic or abiotic synthesis with little free oxygen gas; idea of a prebiotic soup
- Prebiotic chemistry encompassed several hypotheses about where/how organics originated
Stage 1: Reducing atmosphere hypothesis
- Geological data suggest a reducing atmosphere rich in H2O, H2, CH4, NH3 and little O2
- Stanley Miller experiment simulated early Earth conditions with electrical discharges (lightning)
- Result: formation of amino acids, sugars, nitrogenous bases; first major scientific attempt to study origin of life
- Since the 1950s, views on early Earth atmospheres have evolved, but similar results can be obtained under other conditions
Stage 1: Alternative hypotheses and support
- Extraterrestrial hypothesis: meteorites delivered organic carbon (amino acids and nucleic bases) to Earth
- Deep-sea vent hypothesis: temperature gradients between hot vent water and cold ocean water could drive formation of biologically important molecules; vent communities powered by chemical energy (not sunlight); alkaline hydrothermal vents proposed to create pH gradients conducive to organic synthesis
Stage 2: Organic polymers
- Prebiotic synthesis of polymers in aqueous solutions was considered unlikely due to hydrolysis outpacing polymerization
- Experiments showed nucleic acid polymers and polypeptides could form on clay surfaces; later, 2004 experiments demonstrated that polymers can form in aqueous solutions
Stage 3: Polymers enclosed by boundaries (Protobionts)
- Protobiont: aggregate of prebiotically produced molecules/macromolecules with a boundary (e.g., lipid bilayer) that maintains an internal chemical environment distinct from surroundings
- Four defining characteristics:
- Boundary separates external environment from internal contents
- Internal polymers contained information
- Internal polymers had catalytic function
- Protobionts capable of self-replication
Protobionts and liposomes
- Protobionts may have existed as liposomes (vesicles with a lipid bilayer)
- Liposomes can form spontaneously in water and can enclose RNA
- Clay can catalyze liposome formation that can grow and divide
Stage 4: RNA world
- Majority view: RNA likely the first macromolecule of protobionts
- Three key RNA functions required for life-like properties:
- Ability to store information
- Capacity for self-replication
- Enzymatic function (ribozymes)
- DNA and proteins cannot perform all three functions alone
Chemical selection and the RNA world
- Chemical selection: certain molecules in a mixture have properties that favor their increase in number over time
- Hypothetical two-step scenario:
- Step 1: An RNA molecule mutates to gain catalytic ability to attach nucleotides; advantage due to faster self-replication
- Step 2: A second mutation allows synthesis of nucleotides; leads to RNA populations with enhanced catalytic capabilities
- Result: protobionts with multiple catalytic functions (self-replication and nucleotide synthesis) via successive chemical selection
Transition from the RNA world to the DNA/RNA/Protein world
- RNA world eventually gave way to a system where DNA stores information, RNA catalyzes, and proteins perform diverse catalytic and structural roles
Advantages of the DNA/RNA/protein world
- Information storage: DNA provides stable, high-fidelity information storage; relieves RNA of informational burden; DNA is less prone to mutations
- Metabolism and cellular functions: proteins have greater catalytic potential and efficiency; proteins perform diverse tasks (including cytoskeleton and transport)
Microscopy fundamentals (context for cell study)
- Microscopy enables visualization of cell structure; micrograph is an image captured by a microscope
- Key parameters:
- Resolution: ability to distinguish two adjacent objects as separate
- Contrast: differentiation between structures; enhanced by dyes
- Magnification: ratio of image size to actual size
- Two main microscope types by illumination:
- Light microscope: resolution ~0.2 μm
- Electron microscope: resolution ~0.1 nm (2000-fold better than light micrographs)
Size and scale references in cell biology
- The scale of cellular structures spans from atoms (≈0.1 nm) to whole organisms (meters)
- Electron microscopy can resolve atoms up to the size range of organelles (~nm to μm); light microscopy resolves larger features (μm range)
The cell as a system: prokaryotes vs eukaryotes
- Prokaryotes: simple cell structure; no nucleus; two major domains: Bacteria and Archaea
- Eukaryotes: more complex; DNA enclosed within a membrane-bound nucleus; internal membranes form organelles
Prokaryotic cell structure (typical bacterial cell)
- Plasma membrane: double phospholipid layer with embedded proteins; barrier between cytoplasm and environment
- Cytoplasm: internal content of the cell; including cytosol and nucleoid region (DNA location)
- Nucleoid: region where DNA is located (not membrane-bound)
- Ribosomes: synthesize proteins
- Outside the plasma membrane: cell wall provides support and protection; glycocalyx (outer layer) traps water and can help evade the immune system (capsule); appendages include pili (attachment) and flagella (movement)
- Common dimensions: 1–10 μm in diameter for many bacteria
Eukaryotic cell features
- DNA housed inside a membrane-bound nucleus; compartments and organelles with internal membranes; greater structural and functional complexity
- Cytosol as the fluid portion of the cytoplasm outside organelles; endomembrane system and semiautonomous organelles are key components
- Variation in cell morphology across species and cell types; organelles contribute to specialization
The nucleus and endomembrane system
- Nucleus: genome location, gene expression, chromosome organization, and ribosome subunit assembly via nucleolus
- Nuclear envelope: double membrane surrounding the nucleus; nuclear pores regulate transport between nucleus and cytosol
- Endomembrane system: network of membranes including the nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane
Endomembrane system components and functions
- Nuclear envelope: encloses nucleus; serves as part of the endomembrane system with pores for transport
- Endoplasmic reticulum (ER): network of membranes with lumen; two types:
- Rough ER: studded with ribosomes; involved in protein synthesis, sorting, and insertion into ER; glycosylation of proteins and lipids
- Smooth ER: metabolism, detoxification, lipid synthesis, carbohydrate metabolism, calcium ion storage
- Golgi apparatus: stack of flattened compartments (cis, medial, trans)
- Functions: processing, sorting, and secretion; continued glycosylation; proteolysis by proteases; packaging into secretory vesicles for delivery to plasma membrane or extracellular space
- Lysosomes and vacuoles: degradation and storage; lysosomes contain acid hydrolases; vacuoles vary by cell type (central vacuole in plants for storage/volume; contractile vacuoles in protists; phagocytic vacuoles in protists and white blood cells)
- Peroxisomes: catalyze reactions that remove hydrogen or add oxygen; generate and break down hydrogen peroxide via catalase; plant glyoxysomes convert fats to sugars
- Plasma membrane: boundary between cell and environment; selective permeability; cell signaling via receptors; cell adhesion via membrane proteins
The nucleus and endomembrane system in detail
- Nuclear envelope: double membrane with nuclear pores; materials in the nucleus are not part of the endomembrane system
- Chromosomes and chromatin: DNA + proteins forming chromatin; nuclear matrix and lamina organize chromosomes; nucleolus is the ribosome subunit assembly site
- Nuclear pores regulate traffic between nucleus and cytosol
Protein sorting and trafficking in eukaryotic cells
- Eukaryotic proteins often require sorting signals to reach their destinations
- Sorting can be cotranslational (during synthesis) or post-translational (after synthesis)
- Key sorting routes:
- Remain in cytosol if no sorting signal
- Cotranslational sorting to ER: ER signal sequence binds SRP, pauses translation, then translation resumes into ER; proteins may stay in ER or be sent to Golgi via vesicles
- Post-translational sorting to nucleus, mitochondria, chloroplasts, or peroxisomes
- ER signal sequence and SRP receptor guide cotranslational sorting; signal peptidase cleaves the signal sequence once translocation is underway
- Vesicle transport moves cargo between ER, Golgi, lysosomes, plasma membrane, and outside the cell
- Golgi retention signals determine whether proteins stay in Golgi or continue to other destinations
The secretory pathway: Palade experiments and the flow of secreted proteins
- Pulse-chase experiments traced path of radioactive proteins in pancreatic cells
- Findings supported a sequential secretory pathway: ER → Golgi → secretory vesicles → plasma membrane and outside the cell
- Experimental workflow involved radiolabeled amino acids, chase with nonlabeled amino acids, osmium tetroxide staining, EM, and autoradiography to visualize movement
- Conceptual steps showed a consistent flow of proteins through ER and Golgi before secretion
Endomembrane system trajectories in diagrams
- Understanding pathways of cytosolic, cotranslational ER-targeted, and post-translational organelle-targeted proteins
Droplet organelles and phase separation
- Beyond membrane-bound organelles, cells display liquid–liquid phase separation forming droplet-like organelles (e.g., nucleolus) where certain biomolecules concentrate for specific functions
The proteome and cellular identity
- The proteome largely determines cellular characteristics; DNA is the same across different cells, yet cells display different proteomes
- Protein expression levels, isoforms, and post-translational modifications shape cell function
- Proteomes differ between healthy and diseased states (e.g., cancer)
Cell surface area and volume considerations
- As cells increase in size, surface area-to-volume ratio (SA:V) decreases, impacting nutrient uptake and waste export
- Mathematical relation for a sphere:
- Surface area: A = 4 \, \pi \, r^2
- Volume: V = \frac{4}{3} \pi \, r^3
- Therefore, \frac{A}{V} = \frac{4 \pi r^2}{\frac{4}{3} \pi r^3} = \frac{3}{r}
Cytosol and metabolism
- Cytosol is the central coordinating region for metabolic activities in eukaryotic cells
- Metabolism is the sum of all chemical reactions; catalyzed by enzymes in a sequence of steps
- Catabolism: breakdown of molecules
- Anabolism: synthesis of cellular molecules and macromolecules
The cytoskeleton and motor proteins
- Cytoskeleton provides cell shape, organization, and movement
- Three major filament systems:
- Microtubules: hollow tubes made of α- and β-tubulin; dynamic instability; MTOC organizes growth; centrosomes/centrioles in animals; plants lack centrosomes
- Intermediate filaments: tension-bearing, provide structural integrity; keratins and nuclear lamins
- Actin filaments (microfilaments): dynamic with plus/minus ends; support plasma membrane and cell shape
Motor proteins and movement
- Motor proteins use ATP; three-domain structure: head (ATPase and cargo-binding), hinge, tail
- Three movement modes:
- Motor protein carries cargo along a filament
- Filament moves while motor proteins stay in place
- Both motor protein and filament remain fixed, causing bending of the filament
- Common motor proteins and their tracks:
- Kinesin walks along microtubules toward the plus end carrying cargo
- Dynein moves toward the minus end
- Myosin walks along actin filaments (often toward the plus end) to move cargo or reposition the filament
Flagella and cilia
- Flagella: usually longer than cilia; few per cell
- Cilia: shorter, can cover large portions of the cell surface
- Structure: axoneme with a 9+2 arrangement of microtubules; dynein motors and linking proteins generate bending motion
The nucleus and endomembrane system in action
- Nuclear envelope protects genome; double membrane with nuclear pores controls traffic
- Endomembrane system coordinates protein synthesis, sorting, and trafficking
Semiautonomous organelles
- Mitochondria and chloroplasts can grow and divide within the cell
- They depend on the host cell for some internal components but retain their own genomes
Mitochondria
- Primary role: ATP synthesis
- Structure: outer membrane, inner membrane with cristae; intermembrane space and mitochondrial matrix
- Contain their own DNA; divide by binary fission; mitochondrial genome resembles bacterial genomes
Chloroplasts
- Primary role: photosynthesis; found in plants and algae
- Structure: outer/inner membranes, thylakoid membranes, thylakoid lumen, granum stacks, stroma
- Contain their own DNA; divide by binary fission; genomes resemble bacterial genomes
Endosymbiosis and organelle origins
- Modern mitochondria derived from proteobacteria; chloroplasts from cyanobacteria
- Endosymbiosis event: one organism lives inside another; over billions of years, endosymbiotic partners became integrated as organelles
- Evidence: double membranes, own genomes, binary fission-like division, ribosomes similar to bacterial ribosomes
Protein sorting: destination signals
- Eukaryotic proteins often contain sorting signals that direct them to cytosol, nucleus, mitochondria, chloroplasts, peroxisomes, ER, Golgi, lysosomes, or plasma membrane
- Sorting can be cotranslational (ER targeting) or post-translational (other organelles)
- Cotranslational sorting to ER involves the ER signal sequence, SRP, and translocation into the ER lumen; some proteins remain in ER; others go to Golgi via vesicles
- Post-translational sorting involves chaperones and targeting sequences that direct proteins to the nucleus, mitochondria, chloroplasts, or peroxisomes
The secretory pathway (in detail)
- Stepwise movement of proteins destined for secretion:
- Synthesis begins on ribosomes in the cytosol; ER signal sequence directs ribosome to ER; translation paused by SRP and then resumes into the ER
- Within the ER, proteins may be retained by ER retention signals or packaged into vesicles to the Golgi
- In the Golgi, proteins are further processed (glycosylation continues) and sorted; proteins to be secreted are packaged into secretory vesicles
- Secretory vesicles fuse with the plasma membrane to release contents outside the cell
- Palade’s experiments (pulse-chase) traced the path of secreted proteins in pancreatic cells and provided key evidence for the secretory pathway
Post-translational sorting and chaperones
- Proteins destined for nucleus, mitochondria, chloroplasts, or peroxisomes are synthesized in the cytosol and import via specific channels
- Chaperone proteins help keep precursors unfolded to prevent misfolding during import; matrix-targeting sequences guide mitochondrial import, then are cleaved in the matrix
Comparative cell complexity: bacterial vs animal vs plant cells
- Table 4.2 contrasts cell types: presence/absence of endomembrane system, mitochondria, chloroplasts, cell walls, and other features
- Bacteria: no endomembrane system, no nucleus, circular chromosomes; may have cell walls and glycocalyx; SOME species have flagella
- Animal cells: nucleus, endomembrane system, mitochondria, cytoskeleton; no cell wall; diverse organelles
- Plant cells: nucleus, endomembrane system, mitochondria, chloroplasts, large central vacuole; cell wall present
The nucleus and endomembrane system as a coordinated whole
- The nucleus houses most of the genome and coordinates gene expression
- The endomembrane system handles protein processing and trafficking; nuclear envelope is separate from the endomembrane system, but connected via nuclear pores
Summary of key organizational principles
- Cells are organized around energy, matter, organization, and information flow
- Protein–protein interactions generate complex cell architectures
- Information is stored in genomes, but the proteome ultimately determines function and phenotype
- Prokaryotic and eukaryotic cells reflect distinct levels of complexity and organization
Ethical, philosophical, and practical implications
- Understanding origins of cells informs debates about life’s beginnings, the nature of life, and astrobiology
- Endosymbiosis highlights how cooperation between organisms drives major evolutionary transitions
- The study of cellular organization underpins modern biotechnology, medicine, and synthetic biology
Key equations and numerical references
- Surface area to volume ratio for spheres: A = 4\pi r^2, \quad V = \frac{4}{3}\pi r^3, \quad \frac{A}{V} = \frac{4\pi r^2}{\frac{4}{3}\pi r^3} = \frac{3}{r}
- Scale references include: sizes from atoms (≈0.1 nm) to human height (≈2 m) and beyond; electron microscopy can resolve down to ~0.1 nm, while light microscopy resolves larger features (~0.2 μm)
Connections to broader themes
- The transition from RNA world to DNA/RNA/Protein world illustrates a major shift in molecular biology and complexity
- The endomembrane system and endosymbiosis demonstrate how cellular architecture evolves through interconnected processes
- Protein sorting and the secretory pathway exemplify how cells coordinate synthesis and distribution of biomolecules for proper function
Quick recap of foundational terms
- Protobiont, liposome, ribozyme, RNA world, endosymbiosis, mitochondrion, chloroplast, Golgi apparatus, ER, nucleus, nucleolus, chromatin, cytosol, cytoskeleton, microtubules, actin, intermediate filaments, motor proteins (kinesin, dynein, myosin), SRP, ER signal sequence, vesicles, lysosome, peroxisome, vacuole, centrosome, MTOC, centrosome, Gram-positive/negative cell walls, glycocalyx
Note about visual figures and slide-specific details
- Figures 4.1–4.36 illustrate the concepts above, including the Miller-Urey setup, deep-sea vent models, protobionts, RNA world, the secretory pathway, endosymbiosis timelines, organelle structure, proteome organization, and cell architecture
Suggested study tips
- Map out the four stages of the origin of life and be able to explain the evidence for each stage
- Compare and contrast cotranslational vs post-translational sorting with examples
- Draw and label the secretory pathway and trace the path of a secreted protein from ER to plasma membrane
- Memorize the major organelles, their functions, and whether they are membrane-bound or semi-autonomous
- Be able to explain the endosymbiosis theory and the evidence supporting it (own genomes, double membranes, division by fission)
- Understand how SA:V constraints affect cell function and why cells stay small or adopt special shapes
Final takeaway
- The cell is a highly organized system where origin of life, molecular evolution, cellular architecture, and dynamic intracellular transport collectively enable living organisms to function, adapt, and diversify across all domains of life