A2.2 Cell Structure – Comprehensive Study Notes

  • A2.2: Cell Structure – comprehensive study notes (IB Biology)

A. Cells as the basic structural unit of all living organisms (A2.2.1)

  • Core cell theory components:
    • All living things are composed of one or more cells.
    • The cell is the basic unit of life (the smallest unit capable of using energy to sustain a highly ordered state).
    • Cells arise from preexisting cells (no spontaneous generation today, except at origin of life).
  • The Cell Theory as a group of statements that serve as a foundational principle for life on Earth.
  • Viruses are not living and are not made of cells; bacteria, fungi, plants, and animals are cellular and living.
  • Emergent properties: Life emerges from interactions at the cellular level; see emergent properties in C2.2.16 and C3.1.2.
  • Deductive predictions from theory: Based on cell theory, a newly discovered organism is predicted to consist of one or more cells.
  • If something is alive, it is made of cells (and subcellular components alone do not constitute life).
  • In multicellular organisms, the activity of the organism depends on the collective activity of independent cells; cells differentiate into specialized types (A2.2.13) and multicellularity evolved (A2.2.14).

B. Cells and the microscope; microscopy skills (A2.2.2)

  • Skills to develop and practice:
    • Make temporary mounts of cells and tissues; stain samples.
    • Measure sizes using an eyepiece graticule; calculate actual size and magnification.
    • Produce scale bars; take photographs.
  • Measurement as quantitative observation (NOS): measurement with instruments is a form of quantitative observation.
  • Micrographs and notation: ability to identify cell types in light vs electron micrographs; annotate structures.

C. Advanced microscopy (A2.2.3)

  • Developments in microscopy include:
    • Electron microscopy offers higher magnification and resolution than light microscopy.
    • Freeze-fracture and cryogenic electron microscopy (cryo-EM) enable insights into membranes and molecular structure.
    • Fluorescent stains and immunofluorescence in light microscopy provide targeted visualization of proteins and other molecules.
  • Practical implications: electron microscopy is powerful but expensive and often requires fixed, dead samples; light microscopy remains essential for routine teaching and live observations.

D. Structures common to all cells (A2.2.4)

  • Typical features present in prokaryotes and eukaryotes:
    • Plasma membrane: lipid bilayer that separates cell interior from surroundings; fluid mosaic model.
    • Cytoplasm (cytosol): gel-like fluid with water and dissolved solutes; site of metabolic processes.
    • DNA: genetic material; for prokaryotes, naked and not enclosed in a nucleus; for eukaryotes, DNA is in the nucleus wraps around histones.
    • Ribosomes: catalyze protein synthesis; present in both prokaryotes and eukaryotes; 70S in prokaryotes; 80S in eukaryotes.
  • Emergent idea: even though subcellular components exist, life is defined by the cell as a whole and its system of interacting parts.

E. Prokaryote cell structure (A2.2.5)

  • Key components and features to include in diagrams:
    • Cell wall (peptidoglycan in many bacteria; varies; Gram-positive examples include Bacillus and Staphylococcus).
    • Plasma membrane.
    • Cytoplasm.
    • Naked DNA in a loop in the nucleoid region (not membrane-bound).
    • 70S ribosomes.
    • Plasmids (small circular DNA molecules; replicates independently; can carry antibiotic resistance genes; not always present in all prokaryotes).
    • Capsule and Pili: Capsule helps dehydration resistance and adherence; Pili enable attachment, DNA transfer between cells; Some prokaryotes have flagella for locomotion.
  • Variability: prokaryote cell structure varies across species; not all have identical features (e.g., some lack cell walls in phytoplasmas/mycoplasmas).

F. The eukaryote cell (A2.2.6)

  • Common features across eukaryotes:
    • Plasma membrane enclosing a compartmentalized cytoplasm.
    • 80S ribosomes (on free ribosomes and on RER).
    • Nucleus containing chromosomes (DNA wrapped around histones in eukaryotes).
    • Double membrane nuclear envelope with pores.
    • Membrane-bound cytoplasmic organelles: mitochondria, endoplasmic reticulum (RER and SER), Golgi apparatus, lysosomes, vesicles, vacuoles, etc.
    • Cytoskeleton (microtubules and microfilaments).
  • Nucleus and gene expression: DNA in nucleus; transcription occurs in nucleus while translation occurs in cytoplasm; nucleolus synthesizes ribosomal subunits.

G. Unicellular organisms: processes of life (A2.2.7)

  • Core processes shared by all life forms, including unicellular organisms:
    • Homeostasis: maintenance of internal stability; even single cells manage water and solute balance (e.g., Paramecium with contractile vacuoles to remove excess water).
    • Metabolism: sum of all chemical reactions; viruses lack metabolism and are not self-sustaining.
    • Nutrition: autotrophs vs heterotrophs; energy capture and biomass synthesis.
    • Movement: cellular movement and locomotion mechanisms; movement of organelles; cytoskeleton involvement.
    • Excretion: removal of metabolic waste; CO2 as a waste product of respiration; diffusion in unicellular organisms.
    • Growth: increase in size and mass; development and differentiation where relevant.
    • Response to stimuli: chemoreceptors, photoreceptors, thermoreceptors, baroreceptors respond to environmental cues; gene expression can respond to stimuli.
    • Reproduction: unicellular organisms reproduce by binary fission or mitosis; some species undergo sexual processes via fusion or meiosis-like steps.

H. Differences in cell structure among animals, fungi, and plants (A2.2.8)

  • Commonality: all are eukaryotic; cells share core organelles.
  • Differences:
    • Plastids: plants have chloroplasts (photosynthesis); fungi generally lack chloroplasts.
    • Cell walls: plants have cellulose; fungi have chitin; animals lack cell walls.
    • Vacuoles: plants typically have a large central vacuole; animals have small, numerous vacuoles; fungi have vacuoles as well.
    • Centrioles: present in many animal cells; absent in most fungi and vascular plants (though some primitive plants have them).
    • Cilia and flagella: present in many animal cells; less common in fungi/plants; patterns differ (sexual structures in mosses/ferns in some cases).
  • These differences support classification and reflect functional adaptations.

I. Atypical eukaryotes (A2.2.9)

  • Examples illustrate deviations from the typical single-nucleus eukaryotic cell:
    • Aseptate fungal hyphae: multinucleate cytoplasm with no septa.
    • Skeletal muscle fibers: large cells with many nuclei due to fusion of precursor cells.
    • Red blood cells (without nucleus in many vertebrates): anucleate, to maximize oxygen transport surface area.
    • Phloem sieve tube elements: lose nucleus and most organelles; connected to companion cells which retain nucleus.
  • These atypical structures help us understand specialization and limits of the “one nucleus per cell” rule.

J. Electron micrograph skills: A2.2.10 and A2.2.11

  • A2.2.10: identify cell types and structures in light and electron micrographs; key structures to recognize include: nucleoid, prokaryotic cell wall, nucleus, mitochondrion, chloroplast, sap vacuole, Golgi, rough and smooth ER, chromosomes, ribosomes, cell wall, plasma membrane, microvilli.
  • A2.2.11: drawing and annotation of organelles in micrographs; must annotate functions as well as structures.
  • Practice: ability to annotate nucleus, mitochondria, chloroplasts, Golgi, ER, ribosomes, lysosomes, vesicles, vacuoles, secretory vesicles, microvilli, etc.

K. The origin of eukaryotic cells: endosymbiosis (A2.2.12)

  • Key idea: eukaryotes evolved from a common unicellular ancestor with a nucleus; mitochondria evolved by endosymbiosis; some lineages later acquired chloroplasts by endosymbiosis.
  • Evidence includes: presence of 70S ribosomes, naked circular DNA, the ability to replicate; double membranes around mitochondria and chloroplasts; similarity to prokaryotes in size and structure; independent replication within the host cell; sensitivity to antibiotics.
  • The endosymbiotic theory is supported by both structural and functional evidence:
    • Structural: mitochondria and chloroplasts resemble bacteria in size/shape; double membranes.
    • Genetic: circular, naked DNA; 70S ribosomes; similar rRNA gene sequences to prokaryotes.
    • Functional: movement and replication within the host; independence of replication; antibiotic sensitivity.
  • Two main processes proposed for origin:
    • Infolding: internal membranes (ER, Golgi, nuclear envelope) evolved from inward folds of the plasma membrane.
    • Endosymbiosis: aerobic bacteria became mitochondria; photosynthetic bacteria became chloroplasts; symbiotic relationships persisted and became organelles.
  • Endosymbiosis also relates to later organelles’ complexity and distribution across taxa (e.g., chloroplasts in plants and some algae).
  • Ethical/philosophical note: the strength of the theory rests on predictive power and coherence across diverse observations; theories should be questioned but remain robust where evidence supports.

L. Cell differentiation and multicellularity (A2.2.13, A2.2.14)

  • Differentiation: the development of specialized structures and functions in cells; driven by patterns of gene expression, not changes in the DNA sequence itself.
  • Genome concept (A2.2.13/Genome section):
    • The genome is the complete set of genetic information of an organism.
    • Organisms of the same species share most of their genome; all cells within an organism share the same genome.
    • All cells in a multicellular organism have the same genes (though not all genes are expressed in every cell type).
  • Gene expression and housekeeping genes:
    • Of ~20,000 human genes, about 4,000 are expressed in nearly all cell types (housekeeping genes) and support basic cellular functions (cell cycle, DNA replication, metabolism).
  • Regulation of gene expression:
    • Differentiation occurs when different cell types express different genes (D2.2.1).
    • Gene expression involves transcription (DNA to RNA) and translation (RNA to protein).
    • Regulation is controlled by DNA-binding proteins that act as transcription factors, turning genes on or off (D2.2.2).
  • Environmental and hormonal influence on gene expression:
    • External environment (light, temperature, chemicals) and internal signals (hormones, metabolism) can alter gene expression and development (D2.2.6, C2.1.7, C2.1.12).
    • Examples include tyrosinase gene regulation affecting melanin production; Himalayan rabbits and Siamese cats show temperature-sensitive gene expression affecting fur color.
  • Embryonic development and differentiation:
    • Embryonic stem cells (pluripotent) can differentiate into many cell types; DNA methylation can permanently silence some genes while developmental genes become expressed (D2.2.6; B2.3.4).
    • Flower development is guided by shoot apex differentiation with environmental cues like photoperiod and temperature (D3.1.9; C3.1.18).
  • Tissue formation:
    • A tissue is a group of cells that differentiate similarly to perform a shared function.
    • Examples of differentiated tissues: liver, brain, and muscle tissues.
  • Benefits of cell specialization:
    • Cells focus on specific tasks, increasing efficiency and energy efficiency; specialized structures and metabolism support complex organismal functions.
    • Cell size and structure are shaped by specialization (B2.3.5).
  • Evolution of multicellularity:
    • Multicellularity has evolved repeatedly across eukaryotes (animals, plants, fungi, algae).
    • Basic steps: formation of cellular clusters from single cells; then differentiation within the cluster for specialized functions.
    • Two hypotheses for cluster formation:
      1) Independent cells come together to form a cluster.
      2) During division, daughter cells fail to separate, forming a cluster of identical cells.
    • Primitive multicellular life likely involved both processes; clusters can provide selective advantages such to predation resistance, faster resource sharing, and division of labor; clonal clusters such as Volvox and Pleodorina illustrate early differentiation.
  • Genome and development in multicellular organisms drive complexity; cells can become specialized while retaining the ability to reproduce as needed in germ cells.

M. Fossil evidence and timeline of life (A2.2.14; Pgs. 173-175)

  • Fossil evidence of life on Earth:
    • First cells were prokaryotes around 3.5 billion years ago (Ga).
    • First evidence of multicellular life around 2.5 Ga.
  • Multicellularity evolved multiple times across eukaryotic lineages, with many groups containing both unicellular and multicellular species.
  • The evolution of multicellularity involved two key steps:
    1) Clustering of cells from single cells.
    2) Differentiation of cells within clusters into specialized roles.
  • Aggregation of unicellular organisms (biofilms) demonstrates that clonal clustering can be advantageous; quorum sensing coordinates responses in biofilms.

N. Practical: drawing, measurement and microscopy guidelines (A2.2.10, A2.2.11; Guidelines for Drawing Cell Structures)

  • When drawing cell structures seen under a microscope:
    • Use sharp pencils on white unlined paper; avoid shading; include a title with the specimen and lens power; include a scale bar with units.
    • Center the drawing; avoid over-drawing; draw only what is necessary for understanding; do not necessarily draw every detail in the field of view.
    • For high power drawings, show representative cells; indicate wall thickness, membranes, and other key features.
    • The drawing magnification is separate from microscope lens magnification; the drawing magnification should be calculated and clearly labeled.
  • Examples of required labeling and accuracy criteria:
    • Include the scientific name (italicized or underlined) in the title.
    • Provide a scale line and indicate drawing magnification; distinguish between drawing magnification and microscope magnification.
    • Ensure labels are printed, aligned, and organized in a vertical list; avoid cursive.

O. Calculations and formulas (LaTeX)

  • Total magnification of a light microscope:
    ext{Total magnification} = ext{ocular magnification} imes ext{objective magnification}.
  • Example: if ocular = 10× and objective = 4×, then
    ext{Total magnification} = 10\times 4 = 40\,\text{X}.
  • Magnification from image and actual size:
    M = \frac{I}{A},
    where $I$ is the image size and $A$ is the actual size of the specimen.
  • Drawing magnification (for drawings or photographs):
    ext{Drawing magnification} = \frac{\text{size of image (drawing)}}{\text{actual size of specimen}}.
  • Field of view (FOV) considerations:
    • The diameter of the FOV decreases with higher magnification; one can estimate high-power FOV using:
      \text{FOV}{HP} = \frac{\text{FOV}{LP} \times \text{Magnification}{LP}}{\text{Magnification}{HP}}.
  • Unit conversions (quick reference):
    • 1\ \text{mm} = 10^{3}\ \mu\text{m}.
    • 1\ \mu\text{m} = 10^{-6}\ \text{m}.
    • 1\ \text{nm} = 10^{-9}\ \text{m}.

P. Summary of key terms to know

  • Cell theory components; emergent properties; cell as the basic unit of life.
  • Prokaryotic vs eukaryotic cells; organelles and their functions; ribosome types (70S vs 80S);
  • Endosymbiosis and evidence; mitochondria and chloroplasts as endosymbionts.
  • Gene expression and differentiation; housekeeping genes; epigenetic regulation (DNA methylation).
  • Multicellularity and tissue specialization; germ vs somatic cells; evolutionary perspectives.
  • Microscopy techniques, field of view, magnification calculations, and drawing conventions.
  • Atypical cells and exceptions to the single nucleus rule; clonal and colonial examples.
  • Practical connections to real-world biology: endosymbiosis explains origins of mitochondria and chloroplasts; multicellularity enables complex organisms; cell differentiation underpins development and tissue function.

Notes prepared to mirror the content from the transcript, with emphasis on definitions, mechanisms, and practical skills needed for IB Biology A2.2.