IB Biology Topic 5 Notes: Origins of cells, Cell structure, and Viruses (A2.1–A2.3)

Origins of cells (A2.1)

  • Topic scope: Origins of cells, cell structure, and viruses as part of Topic 5 (IB Biology; 1st Assessment 2025).
  • Content statements (AHL A2.1.1–A2.1.9) outline how life’s origins are framed scientifically and the kinds of evidence and methods used to study them.
    • A2.1.1 Conditions on early Earth and the pre‑biotic formation of carbon compounds.
    • A2.1.2 Cells as the smallest units of self-sustaining life.
    • A2.1.3 Challenge of explaining the spontaneous origin of cells, emphasizing that hypotheses must be testable; early Earth conditions cannot be exactly replicated and protocells did not fossilize.
    • A2.1.4 Evidence for the origin of carbon compounds.
    • A2.1.5 Spontaneous formation of vesicles by coalescence of fatty acids into spherical bilayers.
    • A2.1.6 RNA as a presumed first genetic material.
    • A2.1.7 Evidence for a last universal common ancestor (LUCA).
    • A2.1.8 Approaches used to estimate dates of the first living cells and LUCA.
    • A2.1.9 Evidence for the evolution of LUCA near hydrothermal vents.
  • Guiding questions (Page 3):
    • (1) What plausible hypothesis could account for the origin of life?
    • (2) What intermediate stages could there have been between non-living matter and the first living cells?
  • Linking questions: heredity and criteria for evolution by natural selection; necessary conditions for structure to evolve.
  • Core idea: Cells have always operated by the same basic principles; life’s origin remains a testable, multi-theory problem with evidence from chemistry, molecular biology, and geology.

Early Earth conditions and origin of carbon compounds (A2.1.1)

  • Early Earth conditions were not life-sustaining but instrumental for forming biological building blocks.
    • Higher atmospheric temperatures due to greenhouse gases: CO₂ and CH₄ trap infrared radiation, increasing surface temperatures (greenhouse effect).
    • Absence of free oxygen prevented ozone formation; ozone (O₃) protects against UV radiation when formed from O₂ under UV light.
    • UV radiation: without ozone, UV rays reached the surface, causing DNA damage and increasing mutation rates; yet UV energy could drive chemical reactions forming complex organics.
  • Building blocks of life could form from energy inputs:
    • Energy inputs (heat, UV) to atmospheric gas mixtures could yield amino acids, simple sugars, nucleotides, fatty acids.
    • These basic molecules are the building blocks for early cells.
  • Theories proposing pathways to life:
    • Oparin–Haldane “primordial soup” idea: organic molecules formed abiotically in the early atmosphere/ocean and polymerized under energy inputs.
    • UV energy could catalyze the formation of larger polymers (proteins, polysaccharides, RNA, phospholipids).
  • Visual evidence and context: images illustrate ancient cell-like evidence; backstory links to ongoing research.

Cells as the smallest units of self-sustaining life (A2.1.2)

  • Core features of living cells: enclosed by a plasma membrane; store genetic information in DNA; express genes via protein synthesis.
  • Life-defining features (as used in the syllabus):
    • Metabolic reactions (e.g., respiration)
    • Need for nutrition
    • Excretion of metabolic wastes
    • Ability to reproduce and pass genetic information to offspring (allowing evolution by natural selection)
    • Respond to stimuli from external and internal environments
    • Growth
  • Viruses are considered non-living:
    • Lack a cellular structure and organelles; cannot perform metabolic reactions or nutrition.
    • Cannot replicate independently; rely on host cells for replication.
    • Do not carry out life processes on their own.

Challenges and theories of the origin of cells (A2.1.3–A2.1.5)

  • Key challenge: how did the first cells arise spontaneously if they require division of pre-existing cells?
  • Steps inferred for spontaneous origin (from non-living components):
    1) Synthesis of simple organic compounds from inorganic molecules (e.g., Miller–Urey style demonstrations).
    2) Assembly of these polymers into macromolecules (proteins, RNA, polysaccharides, lipids).
    3) Emergence of self-replication capabilities (RNA world-like properties).
    4) Formation of membranes/compartments (lipid bilayers) enclosing polymers with distinct internal chemistries.
  • Theories of origin:
    • Protocell-first theory: spontaneous formation of cell-like compartments (protocells) that could grow and divide; later acquire genetic material (likely RNA).
    • Gene-first theory: spontaneous development of a self-replicating nucleic acid (likely RNA) that then led to cellular membranes and metabolism via natural selection.
    • Metabolism-first theory: life originated as a system of self-sustaining chemical reactions; later membranes and genetic material evolved.
  • Evidence and limitations: multiple lines of evidence and difficult replication of early Earth conditions; lack of fossils for first protocells.
  • Link to RNA world: RNA could store information and catalyze reactions; later DNA and proteins took over genetic storage and catalysis roles, respectively.
  • Miller–Urey experiment (A2.1.4/A2.1.5 context):
    • Recreated prebiotic Earth conditions with a water cycle, reducing atmosphere (mixture of CH₄, NH₃, H₂, etc.), and electric sparks to simulate lightning.
    • After one week, analysis showed traces of simple organic molecules, including amino acids.
    • Significance: demonstrated that organic molecules could form from inorganic precursors under plausible early Earth conditions.
  • Spontaneous vesicle formation (A2.1.5):
    • Fatty acids in water can spontaneously form micelles and vesicles due to amphipathic properties.
    • Vesicles provide compartments with internal chemistry distinct from the environment and can concentrate biomolecules.
  • Critical evaluation of Miller–Urey (Pages 15–15):
    • Methane availability: early Earth atmosphere may have had lower methane than assumed; this challenges the exact atmospheric composition used in the experiment.
    • Energy source: electrical discharge vs UV; for prebiotic chemistry, UV and other energy sources can drive synthesis when combined with CO₂, N₂, and H₂O.
    • Role of water: aqueous environments may hinder polymerization beyond monomer formation and can prevent stable protein formation; water can hinder certain polymerizations.
    • Nucleotides: Miller–Urey did not generate nucleotides; later synthesis of nucleotides required alternative approaches.
  • Spontaneous formation of vesicles by fatty acids into spherical bilayers (A2.1.5) as a plausible step toward protocell membranes.
  • Evolution of membranes and lipid components (A2.1.5; A2.1.3 cross-links):
    • Early membranes likely composed of fatty acids due to their amphipathic nature.
    • Monolayer to bilayer transition occurs with increasing lipid molecules in water; bilayers form vesicles that could encase internal chemistry.
    • Progression toward more complex lipids (glycerol, triglycerides, phospholipids) forms modern cell membranes.
  • RNA world and early genetic material (A2.1.6):
    • RNA may have performed both genetic information storage and catalytic functions in early cells; later, DNA took over storage and proteins (enzymes) took over catalytic roles.

LUCA and origins around hydrothermal vents (A2.1.7–A2.1.9; A2.1.8–A2.1.9)

  • LUCA: Last Universal Common Ancestor; evidence from:
    • Shared biochemistry across all life forms
    • Shared DNA bases and genetic code, and shared amino acids
    • Some genes shared by eubacteria and archaea implying inheritance from LUCA
  • LUCA’s probable characteristics (from molecular and fossil data):
    • Anaerobic (no oxygen)
    • CO₂ to glucose conversion; hydrogen as an energy source; ammonia production for amino acid synthesis
    • Thermophilic (high temperature) adaptation
    • Autotrophic tendencies suggested by fossil/genomic analyses
  • LUCA near hydrothermal vents hypothesis (A2.1.9):
    • Hydrothermal vent environments could provide energy via chemosynthesis and redox gradients suitable for early life.
    • Fossil evidence in Quebec (haematite tubes; 3.77 Ga or possibly older) suggests ancient biological activity near vents.
  • Dating and approaches (A2.1.8):
    • Fossil dating: carbon dating for recent samples (up to ~60,000 years with ¹⁴C); radiometric dating for older rocks.
    • Molecular clock: analyzing DNA mutations over time to estimate divergence times; assumes roughly constant mutation rates.
    • Genome analyses to infer dates of LUCA and early cell evolution.

Ethical, philosophical, and practical implications (A2.1.3 NOS notes)

  • Science emphasizes testability: hypotheses about the origin of life must be testable, even when exact conditions cannot be replicated.
  • The origin of life remains a topic with multiple competing theories; no single universally accepted model yet.
  • The study of early Earth conditions informs our understanding of chemical possibility and limits the range of feasible hypotheses.

Cell structure (A2.2)

  • A2.2.1 Cells as the basic structural unit of all living organisms

    • Cell theory basics: all living organisms are composed of one or more cells; cells are the basic functional units; new cells arise from pre-existing cells.
    • Despite variation in size/shape, all cells have membranes, contain DNA, and carry out enzymatic reactions.
    • Entities such as bacteria (prokaryotes) and eukaryotic cells fit into the theory while noting exceptions in contemporary biology (outside traditional cell theory in rare cases).

  • A2.2.2 Microscopy skills (AOS)

    • Practice: making temporary mounts of cells/tissues; staining; measuring sizes with eyepiece graticule; focusing with coarse and fine adjustments; calculating actual size and magnification; scale bars; photography.
    • Quantitative observations: measurement-based observations support hypotheses and provide numerical data.

  • A2.2.3 Developments in microscopy

    • Two main microscope types: Optical (light) and Electron; each with advantages and limitations.
    • Magnification vs resolution are distinct concepts; resolution is the ability to distinguish two close structures; magnification is image size relative to actual size.

  • A2.2.4 Structures common to cells in all living organisms

    • DNA as genetic material; cytoplasm (cytosol); plasma membrane.
    • DNA enables genetic continuity across generations; DNA controls enzyme production and other vital proteins.
    • Cytoplasm is the site of many cellular reactions; cytosol is the aqueous component.

  • A2.2.5 Prokaryote cell structure

    • Prokaryotes: bacteria (Eubacteria) and archaea; small size (0.1–5.0 μm); no nucleus; DNA typically in a loop; plasmids present; 70S ribosomes; cell wall; cytoplasm; plasma membrane.
    • Archaea membranes can be a single-layered or monolayer structure (different from bacteria).
    • Common prokaryotic features include: 70S ribosomes, naked circular DNA, cytoplasm, plasma membrane, cell wall.

  • A2.2.6 Eukaryote cell structure

    • Eukaryotes have membrane-bound organelles (nucleus, mitochondria, etc.) and compartmentalization that localizes enzymes/substrates and keeps harmful substances segregated.
    • Animal vs plant cells: both have nucleus and mitochondria; plants have chloroplasts, a cellulose cell wall, large vacuoles; animals have centrioles and microvilli; fungi have their own features.
    • Common features: larger 80S ribosomes; endomembrane system (RER, SER, Golgi, vesicles); mitochondria; chloroplasts (plants/algae); lysosomes; vacuoles; centrosomes; cytoskeleton (microtubules).

  • Endosymbiosis and origin of eukaryotes (A2.2.12–A2.2.14)

    • Endosymbiotic theory: eukaryotic cells originated when one cell engulfed another, with the engulfed cell not being digested and instead becoming a symbiont.
    • Evidence for endosymbiosis: mitochondria and chloroplasts replicate by binary fission; have their own circular DNA; ribosomes are 70S; double membranes; separate replication cycles; ribosomes similar to bacterial ones.
    • LUCA context: endosymbiotic events contributed to eukaryotic complexity; endosymbiosis is a powerful theory explaining the origin of organelles.

  • Plant vs animal vs fungal cell differences (A2.2.8–A2.2.9; A2.2.7/A2.2.10)

    • Plant cells: cellulose cell walls; chloroplasts; large permanent vacuoles; plasmodesmata (cytoplasmic connections between plant cells).
    • Animal cells: no cell wall; centrioles; microvilli in some epithelia; membranes flexible.
    • Fungal cells: cell walls rich in glucans and chitin; vacuoles present but often smaller; no chloroplasts.
    • Atypical eukaryotic structures: examples include skeletal muscle fibers (multinucleated), aseptate fungal hyphae (multinucleated with continuous cytoplasm), red blood cells (anucleate in mammals), phloem sieve tubes (no end walls, lack many organelles; companion cells maintain cytoplasm).

  • Organelles and cell components (A2.2.4–A2.2.6; A2.2.9–A2.2.11)

    • Plasma membrane: phospholipid bilayer; semi-permeable; embedded proteins for recognition, signaling, and transport.
    • Nucleus: double membrane; nuclear pores; contains chromatin; nucleolus (ribosome synthesis site).
    • Endoplasmic reticulum: Rough ER has ribosomes (protein synthesis); Smooth ER lacks ribosomes and is involved in lipid synthesis.
    • Ribosomes: 80S in eukaryotes; 70S in prokaryotes; sites of translation; ribosome assembly in nucleolus.
    • Mitochondrion: aerobic respiration site; double membrane with cristae; matrix contains enzymes; mitochondrial DNA and ribosomes.
    • Golgi apparatus: modifies and packages proteins and lipids into vesicles for secretion or delivery to organelles.
    • Lysosome: hydrolytic enzymes for degradation; important in immune response and apoptosis.
    • Chloroplast: site of photosynthesis; double membrane; thylakoids stacked into grana; chlorophyll; circular DNA and ribosomes; occurs in plants.
    • Vacuoles: plant vacuoles large and permanent; animal vacuoles transient; tonoplast membrane.
    • Cell wall: extracellular wall in plants (cellulose) and some fungi/bacteria (peptidoglycan or glucans/chitin); plant plasmodesmata.
    • Cytoskeleton components: microtubules (tubulin: α/β units), microfilaments, intermediate filaments; microvilli and cilia/flagella structures.
    • Peroxisomes, lysosomes, endosomes, vesicles: transport and metabolic roles.

Visual micrograph interpretation and drawing (A2.2.10–A2.2.11)

  • Skills include identifying prokaryotic vs eukaryotic cells, plant vs animal cells, and specific organelles in micrographs (nucleoid, nucleus, mitochondria, chloroplasts, sap vacuole, Golgi, ER, chromosomes, ribosomes, cell wall, plasma membrane, microvilli).

  • Drawing and annotation conventions (A2.2.11):

    • Include title, magnification, scale bar when possible, proper proportion, clear lines, no shading, labeled connections, and function annotations for organelles.

  • Practical notes on reading micrographs (from pages 79–83):

    • Macrophage example (eukaryotic, animal): nucleus, lysosomes, mitochondria, abundant energy needs, etc.
    • Ciliated epithelium of the small intestine example: many mitochondria, microvilli (brush border) for absorption; high energy demands; selective transport.

  • Cell type recognition principles (A2.2.10):

    • Presence/absence of nucleus and cell wall helps categorize as plant, animal, or prokaryote.
    • Organelles present help identify function and tissue type.

  • Basic drawing conventions and units (A2.2.11–A2.2.12)

    • Scale and magnification reporting; relationships between image size and actual size; use of rulers and graticules; standard conventions for labeling.

Endosymbiosis and multicellularity (A2.2.12–A2.2.14; A2.2.7–A2.2.9)

  • Origin of eukaryotic cells by endosymbiosis (A2.2.12)

    • Endosymbiosis: one organism living inside another; mutual benefit preserves the engulfed organism.
    • Endosymbiotic theory explains origin of mitochondria and chloroplasts in eukaryotes.
    • Evolutionary sequence: early prokaryote develops membrane infoldings to increase surface area; then an anaerobic prokaryote engulfs an aerobic prokaryote → mitochondria; later, a photosynthetic prokaryote is engulfed → chloroplasts.
    • LUCA context and later diversification: all eukaryotes share nucleus and organelles with ancestral lineages.
    • Evidence: mitochondria and chloroplasts have their own circular DNA, ribosomes, and replicate by binary fission, dual membranes, and other bacterial-like traits.

  • Cell differentiation and multicellularity (A2.2.13–A2.2.14)

    • Cell compartmentalization allowed specialization; nucleus as a DNA-containing region; energy-producing compartments from endosymbiosis.
    • Multicellularity evolved multiple times; cells differentiate to form tissues, organs, and organ systems; coordination and communication evolve to maintain homeostasis.
    • Benefits of multicellularity: larger size, specialization, efficient functions; difficulties include integration and coordination across tissues.

  • Evidence for and implications of multicellularity (A2.2.14)

    • Tissue examples: epithelial tissue in the intestine (absorption), muscle tissue for movement, etc.
    • Organ systems emerge from coordinated tissues; evolution favors division of labor and more complex regulation.

Viruses (Topic 5C; A2.3)

  • A2.3.1 Structural features common to viruses

    • Viruses are non-cellular infectious particles; not alive by standard criteria because they lack metabolism and independent reproduction.
    • Size: 20–300 nm; visible only by electron microscopy.
    • Genetic material: DNA or RNA; single- or double-stranded; linear or circular.
    • Core components: a nucleic acid core; a protein capsid; sometimes a lipid envelope derived from host membranes; attachment proteins on the surface.
    • Lack cytoplasm and most enzymes; paracite reliance on host ribosomes for protein synthesis.
    • All viruses are parasitic and require a host cell to replicate.

  • A2.3.2 Diversity of structure in viruses

    • Wide variety of genome types and shapes: RNA or DNA; single- or double-stranded; linear or circular.
    • Enveloped vs non-enveloped; shapes can be threadlike, polyhedral, or spherical.
    • Host specificity is determined by attachment proteins that recognize specific receptors on host cells.
    • Examples covered: Bacteriophage lambda (a bacterial virus with a dsDNA genome, tail fibers for adsorption), Coronaviruses (enveloped RNA viruses with a corona-like appearance), HIV (retrovirus with RNA genome and reverse transcriptase).

  • A2.3.3 Lytic cycle of a virus

    • Steps (general):
    • Attachment to host cell via attachment proteins.
    • Injection of viral nucleic acid into host cytoplasm.
    • Biosynthesis using host machinery to produce viral proteins.
    • Assembly of new virions.
    • Release via lysis of the host cell (lysozyme-mediated) or budding in some cases.
    • Outcome: rapid production and dissemination of virions; host cell destruction in lytic path.

  • A2.3.4 Lysogenic cycle of a virus

    • Key difference from lytic cycle: viral DNA integrates into host genome and remains latent as a provirus (prophage).
    • Repressor proteins prevent transcription/translation of viral genes; host cell continues to function and divide, propagating viral DNA.
    • Triggered by environmental cues (e.g., UV exposure, chemicals) to switch to the lytic cycle.
    • Lysogeny allows viral DNA to persist without immediate host damage.

  • A2.3.5 Evidence for several origins of viruses from other organisms

    • The origin of viruses is debated; three main theories:
    • Escape theory: viruses arose from genetic elements (DNA/RNA) that gained mobility between cells and acquired protective envelopes.
    • Regresive/reduction theory: viruses are remnants of cellular organisms or very small cells that became parasites.
    • Virus-first theory: viruses predate their current cellular hosts; simple origins gave rise to modern viruses.
    • Coevolution with hosts and pervasive distribution across life forms; endogenous viral elements are found in genomes (ERVs) indicating long-term host–virus interactions.

  • A2.3.6 Rapid evolution in viruses

    • Viruses evolve rapidly due to high mutation rates, large population sizes, and short generation times (especially RNA viruses).
    • Examples: influenza virus and HIV demonstrate rapid evolution and adaptation.
    • Antigenic drift vs antigenic shift:
    • Antigenic drift: gradual accumulation of small mutations in surface proteins; gradual immune escape (e.g., HIV drift).
    • Antigenic shift: major genetic reassortment when two different viruses co-infect a cell; creates a novel virus not recognized by the host immune system (e.g., some influenza strains).
    • Vaccination implications: drift-vs-shift influences vaccine design and effectiveness; annual updates for slowly drifting viruses; shifts pose bigger vaccine challenges.

  • Practical implications and examples cited

    • Endogenous retroviruses (ERVs) in the human genome illustrate ancient viral DNA integration.
    • Viruses’ dependence on host cell machinery is a central feature across lytic and lysogenic cycles.

  • Connections to broader themes

    • The origin of viruses informs debates about life definitions and the boundaries between living and non-living matter.
    • Viral evolution demonstrates rapid adaptation and coevolution with hosts, illustrating convergent evolutionary pressures across diverse taxa.

Key formulas and numerical notes (LaTeX)

  • Magnification relation (microscopy):
    M = rac{I}{A}
    where M is magnification, I is image size, and A is actual size. All lengths are in the same units.

  • Unit conversions (typical in microscopy contexts):
    1~ ext{μm} = 1000~ ext{nm}
    1~ ext{mm} = 1000~ ext{μm}
    1~ ext{m} = 1000~ ext{mm}

  • LUCA time scale references (as discussed in the transcript):

    • LUCA is estimated to have existed around 4 × 10^9 years ago, with fossil evidence suggesting forms dating to at least 3.77 × 10^9 years ago, possibly older.
    • Modern references place LUCA near the base of the universal tree of life, with evidence drawn from shared biochemistry, DNA bases, and core metabolic features.

Connections to broader themes

  • Continuity and change: From prebiotic chemistry to cellular life and then to complex multicellularity, the notes show a continuum shaped by energy sources, chemistry, and selection pressures.
  • Evidence-based inference: Across origins of life, LUCA, endosymbiosis, and virus origins, scientific understanding relies on multiple lines of evidence (fossils, molecular data, comparative genomics, experimental simulations).
  • Ethical and practical implications: the testability of origin hypotheses; vaccine design in rapidly evolving viruses; the role of endosymbiosis in understanding eukaryotic cell complexity.
  • Real-world relevance: understanding virus structure and lifecycle informs medicine, epidemiology, and biotechnology; insights into cell structure underpin advances in medicine, genetics, and bioengineering.

Quick reference summaries

  • Origins of cells: early Earth chemistry; primordial soup; vesicle formation; RNA world; LUCA; hydrothermal vent hypotheses.
  • Cell structure: cell theory; prokaryotic vs eukaryotic cells; organelles; endosymbiosis; multicellularity; specialized tissues.
  • Viruses: structure, life cycles (lytic vs lysogenic), origins hypotheses, rapid evolution, antigenic drift/shift, vaccines.