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📌Definition Table

Term	Definition
Biological Classification	The systematic arrangement of living organisms into groups based on similarities and evolutionary relationships.
Taxonomy	The science of naming, describing, and classifying organisms.
Systematics	The study of biological diversity and the evolutionary relationships among organisms.
Binomial Nomenclature	A universal naming system assigning each species a two-part name: genus and species.
Taxonomic Hierarchy	The ordered ranking of taxa from broad to specific: domain, kingdom, phylum, class, order, family, genus, species.

📌Introduction

Biological classification provides a framework for organising the immense diversity of life on Earth. By grouping organisms based on shared features and genetic relationships, scientists can communicate effectively, make predictions about unknown species, and understand evolutionary history. The system originated with Carl Linnaeus’s morphological approach and has since evolved to incorporate molecular data, making classification more accurate and reflective of true phylogenetic relationships.

📌 Importance of Classification

• Organises biodiversity into manageable and meaningful groups.
• Enables clear communication among scientists worldwide through standardised naming.
• Provides insights into evolutionary relationships between organisms.
• Helps predict characteristics of newly discovered organisms.
• Supports conservation efforts by identifying species and their roles in ecosystems.
• Facilitates research by grouping organisms with similar traits.

🧠 Examiner Tip: Always italicise genus and species names and capitalise only the genus when writing binomial nomenclature (e.g., Homo sapiens).

📌 Principles of Biological Classification

• Based on observable characteristics and genetic similarities.
• Uses a hierarchical system of ranks from broad to specific.
• Includes both morphological and molecular evidence.
• Reflects evolutionary history wherever possible.
• Employs binomial nomenclature for universal identification.
• Allows for flexibility and revision as new data emerge.

🧬 IA Tips & Guidance: A possible IA could compare species identification using morphological keys versus DNA barcoding techniques.

📌 Types of Classification Systems

• Artificial systems: Based on one or few characteristics, often for convenience (e.g., habitat or size).
• Natural systems: Based on multiple characteristics reflecting evolutionary relationships.
• Phylogenetic systems: Focused on common ancestry using morphological and molecular data.
• Systems can shift as new technologies and evidence become available.
• Phylogenetic classification is currently the most accepted method.
• Fossil evidence can be integrated into classification.

🌐 EE Focus: An EE could analyse how molecular evidence has reshaped classification within a specific group of organisms.

📌 Tools in Biological Classification

• Dichotomous keys for identification.
• Field guides for local species.
• Microscopy for cellular characteristics.
• DNA sequencing for molecular comparisons.
• Bioinformatics for analysing large datasets.
• Phylogenetic software for tree construction.

❤️ CAS Link: A CAS project could involve creating a field guide for local biodiversity, integrating both scientific names and common names.

📌 Limitations and Challenges

• Morphological similarities may be due to convergent evolution, not shared ancestry.
• Genetic data may conflict with traditional classification.
• Hybridisation can blur species boundaries.
• Cryptic species may remain undetected without molecular analysis.
• Classification is dynamic — constant updates are required.
• Human bias can influence early classification decisions.

🔍 TOK Perspective: Classification systems reflect human attempts to impose order on nature; changes in technology and perspective can reshape these systems over time.

📝 Paper 2:
Be ready to define taxonomy and systematics, outline the hierarchy of classification, and compare artificial, natural, and phylogenetic systems.

📌Definition Table

Term	Definition
Domain	The highest taxonomic rank, grouping all life into broad categories based on fundamental genetic and cellular differences.
Archaea	Domain of prokaryotic organisms distinct from bacteria, often living in extreme environments.
Bacteria	Domain of prokaryotic organisms with diverse metabolisms, including many important in ecology and medicine.
Eukarya	Domain containing all organisms with eukaryotic cells (nucleus and membrane-bound organelles).
Kingdom	Taxonomic level below domain, grouping organisms with shared fundamental characteristics.

📌Introduction

The classification of life into domains and kingdoms reflects the deepest evolutionary divisions among organisms. The three-domain system — Bacteria, Archaea, and Eukarya — is based on molecular and genetic evidence, particularly ribosomal RNA sequences. Within each domain, organisms are further divided into kingdoms, reflecting key structural, metabolic, and evolutionary traits. This system captures both ancient divergences in life’s history and the diversity of forms and functions that have evolved since.

📌 The Three Domains

• Bacteria: Prokaryotes with peptidoglycan cell walls, circular DNA, and diverse metabolisms. Examples: Escherichia coli, Streptococcus.
• Archaea: Prokaryotes lacking peptidoglycan, often extremophiles (thermophiles, halophiles, methanogens). Unique membrane lipids and gene expression mechanisms.
• Eukarya: All organisms with eukaryotic cells, including protists, fungi, plants, and animals.
• Domain differences are supported by rRNA sequence comparisons and molecular biology evidence.
• Domains represent the most ancient evolutionary splits, over 3 billion years ago.
• Archaea and Eukarya share more recent common ancestry than either does with Bacteria.

🧠 Examiner Tip: In domain comparisons, always mention cell wall composition, ribosome type, and rRNA sequence differences.

📌 Kingdoms within Domains

• Domain Bacteria: Often grouped into one kingdom (Eubacteria).
• Domain Archaea: Often grouped into one kingdom (Archaebacteria).
• Domain Eukarya: Contains multiple kingdoms:
  • Protista: Mostly unicellular eukaryotes, diverse in form and nutrition.
  • Fungi: Multicellular or unicellular heterotrophs with chitin cell walls.
  • Plantae: Multicellular autotrophs with cellulose cell walls, photosynthetic.
  • Animalia: Multicellular heterotrophs without cell walls, complex body plans.
• Modern research suggests Protista is paraphyletic, with groups reclassified based on molecular data.
• Kingdom classification can vary depending on system used (e.g., 5-, 6-, or more kingdoms).

🧬 IA Tips & Guidance: A possible IA could investigate environmental conditions affecting growth rates of representative organisms from different domains.

📌 Characteristics of Domains and Kingdoms

• Bacteria: Binary fission reproduction, 70S ribosomes, sensitive to traditional antibiotics.
• Archaea: Resistant to most antibiotics, unique lipid monolayers in membranes, ability to survive extreme conditions.
• Eukarya: Mitotic and meiotic cell division, 80S ribosomes in cytoplasm, membrane-bound organelles.
• Fungi: Absorptive nutrition, decomposers, important in symbiosis (mycorrhizae).
• Plantae: Photosynthetic autotrophs, alternation of generations life cycle.
• Animalia: Nervous and muscular systems for rapid response and movement.

🌐 EE Focus: An EE could compare molecular phylogenies of organisms from different domains to test evolutionary relationships suggested by rRNA evidence.

📌 Evolutionary Basis of Domains

• Carl Woese introduced the three-domain system in the late 20th century.
• Based on sequencing of the 16S and 18S rRNA genes.
• Revealed Archaea are genetically closer to Eukarya than to Bacteria.
• Supports the idea of a universal common ancestor.
• Highlights the importance of molecular data in reshaping classification.
• Suggests early life experienced horizontal gene transfer, complicating lineage tracing.

❤️ CAS Link: A CAS activity could involve creating an illustrated timeline of the evolutionary emergence of domains and kingdoms for a school biology exhibition.

📌 Applications of Domain and Kingdom Classification

• Medical: distinguishing between bacterial and archaeal pathogens for correct treatment.
• Environmental: identifying microbial communities in extreme environments.
• Evolutionary research: tracing the origin of complex cellular features.
• Conservation: cataloguing biodiversity for protection.
• Biotechnology: selecting species with useful enzymes (e.g., thermostable DNA polymerase from Thermus aquaticus in Archaea).
• Education: simplifying biological diversity into a teachable structure.

🔍 TOK Perspective: The division of life into domains shows how advances in technology (DNA sequencing) can reshape scientific classification systems and challenge traditional frameworks.

📝 Paper 2:
Be ready to compare domains in a table, give examples from each kingdom, and explain molecular evidence supporting the three-domain system.

📌Definition Table

Term	Definition
Taxonomy	The science of classifying organisms into groups based on shared characteristics.
Binomial Nomenclature	The two-part scientific naming system for species, consisting of genus and species names.
Taxon (plural: taxa)	A group of organisms classified together at any level in the taxonomic hierarchy.
Phylogeny	The evolutionary history and relationships among species.
Cladistics	A classification method that groups organisms by common ancestry using shared derived characteristics.

📌Introduction

Classification and taxonomy organise biological diversity into a structured system, enabling scientists to identify, name, and study organisms systematically. This framework allows communication across languages and disciplines and reflects evolutionary relationships. The modern system of taxonomy, developed from the work of Carl Linnaeus, uses hierarchical levels — from domain to species — and binomial nomenclature for species naming. Advances in molecular biology have refined classification, allowing genetic data to guide taxonomy and resolve ambiguities in evolutionary relationships.

📌 Taxonomic Hierarchy

• Levels from broadest to most specific: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species.
• Each level groups organisms with increasingly specific similarities.
• Binomial nomenclature: genus name capitalised, species name lowercase (e.g., Homo sapiens).
• Classification reflects morphological, physiological, and molecular traits.
• Fossil records and molecular clocks can support taxonomic placement.
• Revisions occur as new data become available, especially from DNA sequencing.

🧠 Examiner Tip: Always italicize scientific names in written answers and ensure the genus is capitalised but the species name is not.

📌 Principles of Classification

• Morphological classification: based on structural similarities and differences.
• Physiological classification: based on metabolic processes or biochemical traits.
• Molecular classification: uses DNA, RNA, or protein sequence comparisons.
• Ecological classification: based on habitat or ecological niche.
• Cladistic analysis: groups organisms by evolutionary descent rather than overall similarity.
• Classification systems are dynamic, changing with new discoveries.

🧬 IA Tips & Guidance: A possible IA could compare classification outcomes when using morphological vs molecular data for the same set of species.

📌 Cladistics and Phylogenetic Trees

• Cladograms depict evolutionary relationships based on shared derived characteristics (synapomorphies).
• Branch points (nodes) represent common ancestors.
• Outgroups help establish the direction of evolutionary change.
• Molecular phylogenetics uses DNA/RNA/protein data to build trees.
• Trees are hypotheses, subject to change with new evidence.
• Cladistics emphasises monophyletic groups (common ancestor and all its descendants).

🌐 EE Focus: An EE could analyse how molecular phylogenetics has changed the classification of a specific group (e.g., fungi or protists).

📌 Advantages of Taxonomy

• Provides a universal language for scientists worldwide.
• Organises vast biodiversity into manageable categories.
• Reflects evolutionary relationships between organisms.
• Facilitates identification of species and study of their biology.
• Aids in predicting characteristics of newly discovered organisms.
• Helps track and manage biodiversity conservation efforts.

❤️ CAS Link: A CAS project could involve creating an interactive exhibit on classification for a local science fair.

📌 Tools and Methods in Taxonomy

• Dichotomous keys for species identification.
• Field guides for local flora and fauna.
• Genetic barcoding using standard DNA sequences.
• Microscopy to examine structural features.
• Biochemical assays for unique metabolic products.
• Databases like GenBank for genetic information.

🔍 TOK Perspective: Taxonomy illustrates how scientific classification systems are human-made frameworks that reflect both nature and our interpretation of it — they can change as new knowledge emerges.

📝 Paper 2:
Be prepared to construct or interpret a cladogram, explain binomial nomenclature, and compare morphological vs molecular classification methods.

📌Definition Table

Term	Definition
Virus Origin Hypotheses	Theories explaining how viruses first appeared, including progressive, regressive, and coevolution hypotheses.
Progressive Hypothesis	Suggests viruses evolved from mobile genetic elements (e.g., plasmids, transposons) that gained the ability to move between cells.
Regressive Hypothesis	Proposes viruses evolved from more complex parasitic cells that lost genes over time, becoming dependent on hosts.
Coevolution Hypothesis	Suggests viruses evolved alongside the first cellular life forms from self-replicating molecules.
Viral Quasispecies	A group of viruses with related but genetically varied genomes, arising from high mutation rates, especially in RNA viruses.

📌Introduction

The origin of viruses remains a subject of debate, as they leave no fossil record and their nature blurs the boundary between living and non-living entities. Several hypotheses attempt to explain their emergence, including evolution from mobile genetic elements (progressive), degeneration from more complex ancestors (regressive), or coevolution with the earliest life forms. Viruses have been present for billions of years, evolving alongside their hosts, influencing genetic diversity, and playing significant roles in ecosystems. Their rapid mutation rates and capacity for horizontal gene transfer make them key drivers of evolution.

📌 Progressive Hypothesis

• Viruses originated from fragments of cellular genetic material, such as plasmids or transposons.
• These mobile genetic elements gained the ability to exit one cell and enter another, possibly via protein coats.
• Explains similarities between some viral genes and host cell genes.
• Supported by the existence of retrotransposons, which share mechanisms with retroviruses.
• Suggests viruses are derived from their hosts, not ancient life forms.
• Fits well with RNA viruses, which may have arisen from RNA-based replicators in early cells.

🧠 Examiner Tip: If asked to compare hypotheses, always mention supporting evidence and key limitations — IB rewards balanced evaluation.

📌 Regressive Hypothesis

• Proposes that viruses were once free-living, parasitic cells that lost genes over time.
• As dependence on hosts increased, unnecessary genes for metabolism and independent survival were discarded.
• Explains large DNA viruses like mimiviruses, which have genes similar to cellular organisms.
• Suggests a continuum between viruses and intracellular parasites.
• Limited by lack of direct fossil or molecular evidence.
• Implies multiple independent origins for different virus groups.

🧬 IA Tips & Guidance: A literature-based IA could compare genomic features of giant viruses and parasitic bacteria to investigate gene loss patterns.

📌 Coevolution Hypothesis

• Suggests viruses arose from self-replicating molecules in the pre-cellular “RNA world.”
• Viruses and cells may have evolved together, influencing each other’s development.
• Implies viruses are as ancient as life itself.
• Supported by similarities between some viral enzymes and those in ancient cellular lineages.
• Could explain unique viral proteins with no known cellular counterpart.
• Suggests an ancient role for viruses in shaping genetic systems.

🌐 EE Focus: An EE could explore whether coevolutionary evidence supports a universal viral ancestor or multiple independent origins.

📌 Viral Evolutionary Dynamics

• RNA viruses evolve rapidly due to high mutation rates.
• Genetic recombination between viruses and hosts occurs frequently.
• Viruses can acquire host genes, influencing host evolution.
• Viral quasispecies ensure adaptability to changing environments.
• Coevolutionary “arms races” occur between viruses and host immune systems.
• Some viral sequences have been incorporated into host genomes (endogenous retroviruses).

❤️ CAS Link: A CAS project could involve creating an educational documentary explaining how viruses shape biodiversity and evolution.

📌 Evidence and Challenges

• No direct fossil record, but viral structures can be inferred from molecular data.
• Ancient viral DNA found integrated into host genomes offers evolutionary clues.
• Comparative genomics reveals relationships between viral and cellular genes.
• Lack of universal viral genes makes determining a single origin difficult.
• Likely that different virus families have different evolutionary pathways.
• Studying viruses from extreme environments may reveal ancient features.

🔍 TOK Perspective: The debate over viral origins highlights how different interpretations of the same evidence can lead to competing theories in science.

📝 Paper 2:
Expect questions asking you to compare origin hypotheses, link evidence to specific examples, and explain how viral evolution affects disease emergence.

📌Definition Table

Term	Definition
Lytic Cycle	Viral replication process in which the host cell is lysed to release new virus particles.
Lysogenic Cycle	Viral replication strategy in which the viral genome integrates into the host genome and remains dormant before activation.
Reverse Transcriptase	Enzyme used by retroviruses to convert RNA into DNA inside the host cell.
Provirus	Viral DNA integrated into the host’s genome during lysogeny.
Host Range	The variety of organisms or cell types a virus can infect, determined by receptor compatibility.

📌Introduction

Viruses cannot reproduce independently and must use the machinery of a host cell to replicate. The replication process varies depending on the virus type, genome composition, and host. Two main replication pathways are observed in bacteriophages: the lytic cycle, which rapidly destroys the host cell, and the lysogenic cycle, which allows the virus to persist in a dormant state before activation. Animal viruses may enter via membrane fusion or endocytosis, while bacteriophages inject their DNA directly. Retroviruses like HIV have unique replication mechanisms involving reverse transcription.

📌 The Lytic Cycle

• Virus attaches to host cell via specific receptor proteins.
• Viral genome enters the cell (injection for bacteriophages, fusion/endocytosis for animal viruses).
• Host cell machinery is hijacked to replicate viral nucleic acids and synthesise viral proteins.
• New viral particles are assembled in the cytoplasm.
• Host cell bursts (lysis), releasing many new viruses to infect other cells.
• This cycle results in rapid spread but also rapid destruction of host cells.

🧠 Examiner Tip: For IB diagrams, ensure the lytic cycle steps are in the correct order and labelled clearly with terms like “assembly” and “lysis”.

📌 The Lysogenic Cycle

• Viral genome integrates into host DNA, forming a provirus (or prophage in bacteria).
• The provirus is replicated along with the host’s DNA during cell division.
• No immediate damage occurs to the host cell.
• Environmental triggers (e.g., UV light, stress) can activate the virus.
• The provirus then enters the lytic cycle, producing new viruses.
• Lysogeny allows long-term persistence within the host population.

🧬 IA Tips & Guidance: A safe simulation IA could model virus spread using computer software, comparing lytic and lysogenic replication rates.

📌 Retrovirus Replication (HIV Example)

• Virus binds to specific receptors (e.g., CD4 and CCR5 on helper T cells).
• Viral RNA and enzymes enter the host cell.
• Reverse transcriptase converts viral RNA into DNA.
• Viral DNA integrates into the host genome as a provirus.
• Host cell transcribes and translates viral genes to make new viral proteins.
• New virions assemble and bud from the host cell, often without immediate lysis.
• Antiretroviral drugs target reverse transcriptase or other replication steps.

🌐 EE Focus: An EE could investigate the effectiveness of different antiviral drugs in inhibiting specific stages of viral replication.

📌 Factors Affecting Replication Speed

• Type of genome: RNA viruses generally replicate faster than DNA viruses.
• Host cell type: actively dividing cells often support faster replication.
• Immune system status: weakened immunity can allow faster viral spread.
• Presence of antiviral drugs: can slow or block replication steps.
• Environmental triggers: can activate dormant lysogenic viruses.
• Viral load: higher initial dose can lead to faster onset of symptoms.

❤️ CAS Link: A CAS project could involve designing an educational game that simulates the spread of lytic vs lysogenic viruses.

📌 Microscopy and Molecular Tools in Studying Replication

• TEM visualises viral assembly stages inside host cells.
• Fluorescent tagging tracks viral protein movement in real time.
• PCR detects and quantifies viral genomes in infected cells.
• Western blotting identifies viral proteins during replication.
• Cell culture allows controlled study of infection cycles.
• Data from these methods support antiviral drug development.

🔍 TOK Perspective: The study of viral replication shows how models and simulations help scientists understand processes too small or rapid to observe directly.

📝 Paper 2:
Be able to diagram the lytic and lysogenic cycles, explain retrovirus replication, and discuss how replication strategies influence disease progression.

📌Definition Table

Term	Definition
Virus	A non-cellular infectious particle composed of genetic material enclosed in a protein coat; considered acellular as they lack metabolism.
Capsid	Protein coat surrounding viral genetic material, often with attachment proteins for host cell recognition.
Envelope	Lipid bilayer surrounding some viruses, derived from host cell membranes, often containing glycoproteins.
Attachment Proteins	Molecules on the viral surface that bind to specific receptors on host cells.
Retrovirus	RNA virus (e.g., HIV) that uses reverse transcriptase to produce DNA from its RNA genome.

📌Introduction

Viruses are acellular infectious agents that occupy a unique position in biology — they are not considered living organisms because they lack cellular structures, metabolism, and independent reproduction. Instead, they hijack the machinery of host cells to replicate. They are extremely small, with sizes typically between 20–300 nm, visible only under an electron microscope. Despite their simplicity, viruses exhibit remarkable diversity in shape, genetic material, and infection strategies. Their ability to infect nearly all forms of life makes them central to studies in medicine, genetics, and evolutionary biology.

📌 General Structure of Viruses

• All viruses have a nucleic acid genome made of DNA or RNA, which may be single- or double-stranded, linear or circular.
• The genome is enclosed in a capsid made of protein subunits (capsomeres).
• Attachment proteins on the capsid or envelope bind specifically to host cell receptors.
• Many animal viruses have a lipid envelope derived from the host cell membrane; some plant and bacteriophage viruses are non-enveloped.
• Viruses have no cytoplasm, organelles, or metabolic enzymes (or very few).
• They are parasitic, relying entirely on the host cell’s ribosomes and energy for replication.

🧠 Examiner Tip: Always specify the type of nucleic acid and whether the virus is enveloped when describing its structure — IB markschemes reward these details.

📌 Structural Diversity

• Genetic material can be RNA or DNA, single- or double-stranded.
• Shapes include helical, polyhedral, complex, and spherical.
• Host range is determined by specific attachment proteins — e.g., HIV targets helper T cells, hepatitis viruses target liver cells.
• Bacteriophage lambda: infects E. coli, has dsDNA, capsid head, tail, and tail fibres for DNA injection.
• Coronavirus: ssRNA, spherical, envelope with spike glycoproteins forming a “crown” appearance.
• HIV: retrovirus with two RNA strands, reverse transcriptase, protein capsid, and envelope from host cell membrane.

🧬 IA Tips & Guidance: For a practical investigation, model virus structures using 3D printing or software, emphasising differences between enveloped and non-enveloped viruses.

📌 Special Features in Some Viruses

• Enzymes such as reverse transcriptase (in retroviruses) or lysozyme (in bacteriophages).
• Tail fibres in bacteriophages for host recognition.
• Glycoproteins for immune evasion and host entry.
• Segmented genomes in some viruses (e.g., influenza), allowing genetic reassortment.
• Capsid symmetry (icosahedral, helical, complex) influences stability and infectivity.
• Envelope proteins can determine virus transmissibility.

🌐 EE Focus: An EE could investigate structural adaptations in viruses that enable cross-species transmission, such as changes in surface glycoproteins.

📌 Functional Importance of Structure

• Capsid protects viral genome from degradation.
• Attachment proteins ensure host specificity.
• Envelope lipids aid entry into host cells via membrane fusion.
• Genome type influences replication strategy (RNA viruses often mutate faster).
• Structural variation determines environmental stability (non-enveloped viruses survive longer outside hosts).
• Viral structure can influence immune system evasion strategies.

❤️ CAS Link: A CAS project could involve creating educational campaigns on viral structure and transmission prevention during flu season.

📌 Microscopy in Virus Study

• Electron microscopy is required due to small size.
• TEM reveals internal viral structures, capsid arrangement, and genome location.
• SEM provides 3D images of virus surface morphology.
• Cryo-electron microscopy enables near-atomic resolution structural analysis.
• Structural knowledge is critical for vaccine design.
• Light microscopy cannot resolve individual viruses due to resolution limits (~200 nm).

🔍 TOK Perspective: The study of viruses illustrates how limitations in technology constrain what we can know — before electron microscopy, viruses were only hypothesised based on disease patterns.

📝 Paper 2:
Be prepared to draw and label a virus, describe structural features of specific examples (HIV, bacteriophage, coronavirus), and link structure to function and host specificity.

📌Definition Table

Term	Definition
Eukaryote	An organism whose cells contain a nucleus and membrane-bound organelles. Includes plants, animals, fungi, and protists.
Endomembrane System	Network of membranes within the cell that synthesises, processes, and transports molecules.
Cytoskeleton	Network of protein filaments providing structural support, intracellular transport, and cell movement.
Endosymbiotic Theory	Hypothesis that mitochondria and chloroplasts originated from free-living prokaryotes engulfed by ancestral eukaryotic cells.
80S Ribosomes	Larger ribosomes found in eukaryotic cytoplasm, responsible for protein synthesis.

📌Introduction

Eukaryotic cells are more structurally complex than prokaryotes, containing a true nucleus and numerous membrane-bound organelles. This compartmentalisation allows for greater efficiency in metabolic processes and supports the specialised functions required by multicellular organisms. Eukaryotic cells are thought to have evolved through endosymbiosis, where ancestral cells incorporated prokaryotes that became permanent organelles such as mitochondria and chloroplasts. Their complexity enables functions such as coordinated signalling, advanced locomotion, and large-scale structural organisation in tissues and organs.

📌 Structure of Eukaryotic Cells

• Nucleus enclosed by a double membrane, containing DNA and nucleolus for ribosome synthesis.
• Endoplasmic reticulum (ER): rough ER (with ribosomes) synthesises proteins; smooth ER synthesises lipids and detoxifies toxins.
• Golgi apparatus modifies, sorts, and packages proteins and lipids for secretion or intracellular use.
• Mitochondria produce ATP through aerobic respiration, containing their own DNA and 70S ribosomes.
• Chloroplasts (in plants/algae) perform photosynthesis and also contain their own DNA and 70S ribosomes.
• Cytoskeleton (microtubules, microfilaments, intermediate filaments) maintains cell shape and enables transport.

🧠 Examiner Tip: Always mention that mitochondria and chloroplasts have double membranes and their own DNA/ribosomes as evidence for endosymbiotic theory.

📌 Endosymbiotic Theory Evidence

• Mitochondria and chloroplasts are similar in size to prokaryotes.
• Both have double membranes, consistent with engulfing events.
• Both contain circular DNA like bacteria.
• Both have 70S ribosomes, not 80S like the rest of the eukaryotic cell.
• They replicate independently via binary fission.
• Antibiotics that target bacterial ribosomes can also affect these organelles.

🧬 IA Tips & Guidance: An IA could test effects of specific antibiotics on chloroplast activity in algae to model bacterial ribosome inhibition.

📌 Specialised Eukaryotic Structures

• Cilia and flagella for movement (9+2 microtubule arrangement).
• Lysosomes contain hydrolytic enzymes for digestion and recycling of cellular components.
• Peroxisomes detoxify harmful substances and perform lipid metabolism.
• Vacuoles in plant cells store water, nutrients, and waste.
• Cell wall in plants, fungi, and some protists provides structural support.
• Extracellular matrix (ECM) in animal cells helps with adhesion and signalling.

🌐 EE Focus: An EE could investigate differences in cytoskeletal arrangements between animal and plant cells and how they relate to cell shape and function.

📌 Functions of Eukaryotic Cells

• Genetic control through regulated transcription and translation.
• Energy transformation in mitochondria and chloroplasts.
• Macromolecule synthesis in ER and Golgi apparatus.
• Intracellular transport via vesicles and cytoskeletal tracks.
• Signal transduction through receptor-ligand interactions at the plasma membrane.
• Specialisation in multicellular organisms for tissue-specific functions.

❤️ CAS Link: A CAS activity could involve designing 3D models of eukaryotic cells for educational workshops in local schools.

📌 Microscopy in Eukaryotic Studies

• Light microscopy reveals overall cell structure, organelles like chloroplasts and nucleus.
• Transmission electron microscopy (TEM) shows internal details like cristae in mitochondria.
• Scanning electron microscopy (SEM) provides 3D surface images of cells.
• Fluorescence microscopy highlights specific organelles or proteins with dyes or GFP.
• Confocal microscopy produces sharper, layered images of thick specimens.
• Advances in microscopy have deepened our understanding of eukaryotic compartmentalisation.

🔍 TOK Perspective: The endosymbiotic theory demonstrates how combining molecular, structural, and evolutionary evidence can strengthen a scientific explanation.

📝 Paper 2:
Expect to compare eukaryotic and prokaryotic cells, describe organelle functions, and use structural evidence to explain endosymbiotic theory.

📌Definition Table

Term	Definition
Prokaryote	Single-celled organism lacking a membrane-bound nucleus and organelles. Includes Bacteria and Archaea.
Plasmid	Small, circular DNA molecule separate from chromosomal DNA, often carrying extra genes like antibiotic resistance.
Nucleoid	Region in a prokaryotic cell where the circular DNA is located, not enclosed by a membrane.
Pilus (pili)	Hair-like appendages on prokaryotes used for attachment or DNA transfer during conjugation.
Binary Fission	Asexual reproduction process in prokaryotes where the cell divides into two identical cells.

📌Introduction

Prokaryotic cells are the most ancient and structurally simple forms of life, appearing on Earth over 3.5 billion years ago. They lack a true nucleus and membrane-bound organelles, yet they perform all essential life functions such as metabolism, growth, and reproduction. Their compact and efficient structure allows them to thrive in diverse environments, from deep-sea vents to the human gut. Understanding prokaryotic cell structure is key to microbiology, biotechnology, and medicine, as many prokaryotes are either beneficial (e.g., nitrogen-fixing bacteria) or harmful (pathogens).

📌 Structure of Prokaryotic Cells

• Cell wall composed of peptidoglycan (in Bacteria) or other polymers (in Archaea), providing shape and protection.
• Plasma membrane controls movement of substances in and out of the cell.
• Nucleoid contains a single, circular DNA molecule, the main genetic material.
• Plasmids carry extra genes, often conferring survival advantages.
• Ribosomes (70S) are the sites of protein synthesis.
• Flagella enable motility, powered by a rotary motor mechanism.
• Pili and fimbriae assist in attachment to surfaces and in conjugation.

🧠 Examiner Tip: Always specify 70S ribosomes when describing prokaryotic cells in IB exams, as it’s a common marking point.

📌 Reproduction & Gene Transfer

• Prokaryotes reproduce asexually via binary fission, producing genetically identical cells.
• DNA is replicated starting at a single origin of replication before cell division.
• Conjugation allows DNA transfer between prokaryotes via pili.
• Transformation occurs when prokaryotes absorb foreign DNA from the environment.
• Transduction uses viruses (bacteriophages) to transfer genetic material between cells.
• These methods contribute to rapid adaptation and evolution in bacterial populations.

🧬 IA Tips & Guidance: For a lab investigation, bacterial growth curves can be measured under different environmental conditions, linking cell structure to survival.

📌 Specialized Structures in Some Prokaryotes

• Capsule: protective layer preventing desiccation and aiding immune evasion.
• Endospores: dormant, resistant structures for surviving extreme conditions.
• Thylakoid membranes in cyanobacteria for photosynthesis.
• Magnetosomes for orientation in magnetic fields.
• Gas vesicles for buoyancy control in aquatic environments.
• Plasma membrane infoldings to increase surface area for metabolic processes.

🌐 EE Focus: An EE could explore structural adaptations of extremophilic prokaryotes and how these allow survival in extreme environments.

📌 Functions of Prokaryotic Cells

• Maintain homeostasis through selective permeability of the plasma membrane.
• Perform metabolism, including respiration, fermentation, and photosynthesis (in some species).
• Protect against environmental stress through cell wall and capsule formation.
• Engage in symbiotic relationships (e.g., gut microbiota in humans).
• Adapt rapidly to environmental change via high mutation rates and horizontal gene transfer.
• Act as decomposers, nitrogen fixers, and producers in ecosystems.

❤️ CAS Link: A CAS project could involve creating public awareness materials on antibiotic resistance, linking bacterial gene transfer to public health.

📌 Microscopy in Prokaryotic Studies

• Light microscopes allow observation of general shape and arrangement of cells.
• Electron microscopes reveal internal details, such as ribosomes and nucleoid structure.
• Staining techniques (Gram staining) differentiate bacterial cell wall types.
• Fluorescence microscopy can highlight specific proteins or DNA sequences.
• Time-lapse microscopy can show binary fission in real time.
• Microscopy is essential for taxonomy, pathology, and research into cell function.

🔍 TOK Perspective: Our understanding of prokaryotic cells depends heavily on technological advancements in microscopy — without these tools, much of modern microbiology would not exist.

📝 Paper 2:
Be ready to draw and label a prokaryotic cell, distinguish between Bacteria and Archaea, and describe binary fission and horizontal gene transfer mechanisms.