Cell Structure
Foundations of cell biology: light and electron microscopy with magnification calculations, eukaryotic cell organelles in plants and animals, prokaryotic cell features, and the non-cellular nature of viruses.
The microscope in cell studies
Microscopy is the foundational practical skill for AS & A Level Biology. Whether examining tissue slides for Topic 1, photosynthetic pigments for Topic 13, or kidney sections for Topic 14, every candidate is expected to prepare slides, draw cells, calibrate measurements, and calculate magnifications and actual sizes using mm, µm, and nm.
Specimen preparation and drawing
For temporary mounts viewed under the light microscope, candidates should be able to perform the standard sequence: collect a thin specimen, place it on a clean slide with a drop of stain or water, lower a coverslip at an angle from one edge to exclude air bubbles, and blot excess fluid. Common stains include iodine (starch in plant cells), methylene blue (animal cell nuclei), and aceto-orcein (chromosomes).
- Use a sharp pencil — no shading or sketchy multiple lines
- Lines must be single, continuous, and connect cleanly
- Label every structure with horizontal label lines (no arrows)
- Show only what is actually visible — do not add textbook detail
- Include a scale bar OR magnification statement (never both)
- Title with specimen + plane of section + objective lens used
Low-power plan: shows tissue layout and boundaries between regions. No individual cells drawn.
High-power detail: shows individual cells with visible organelles. Typically only 3–5 representative cells.
Magnification calculation
The fundamental relationship the syllabus expects candidates to apply fluently:
Therefore: Actual size = Image size ÷ Magnification
And: Image size = Actual size × Magnification
Critical: Image size and actual size must be in the same unit before dividing. Convert first, then calculate.
An electron micrograph shows a mitochondrion measuring 28 mm long. The stated magnification is ×14 000. Calculate the actual length in µm.
Step 1 — Convert image size to µm: 28 mm = 28 000 µm
Step 2 — Apply formula: Actual size = 28 000 µm ÷ 14 000 = 2.0 µm
Mitochondria are typically 1–10 µm long, so 2.0 µm is biologically plausible — always sense-check against known organelle sizes.
Unit conversions for microscopy
| Unit | Symbol | Value in metres | Typical use |
|---|---|---|---|
| millimetre | mm | 10−3 m | Whole organisms; small tissues |
| micrometre | µm | 10−6 m | Cells (10–100 µm); organelles (1–10 µm) |
| nanometre | nm | 10−9 m | Membranes (~7 nm); ribosomes (~25 nm); viruses (20–300 nm) |
Conversion shortcuts to memorise: 1 mm = 1000 µm = 1 000 000 nm. To convert mm to µm, multiply by 1000. To convert µm to nm, multiply by 1000.
Eyepiece graticule and stage micrometer
An eyepiece graticule is a small ruler etched onto a glass disc inside the eyepiece. Its divisions (epu — eyepiece units) appear superimposed on any specimen. But each epu has a different real-world value at each magnification — so it must be calibrated against a stage micrometer: a slide with a precise scale (typically 1 mm divided into 100 divisions of 10 µm each).
- Place stage micrometer on stage; focus until both scales are visible.
- Align the two scales so divisions line up (both ideally at left).
- Count how many epu match a known number of stage micrometer divisions.
- Calculate:
1 epu = (stage divisions × 10 µm) ÷ epu count - Repeat for each objective lens used (×4, ×10, ×40).
Under the ×40 objective, 50 eyepiece divisions span 4 stage micrometer divisions. Calculate the value of 1 eyepiece division in µm.
Step 1: 4 stage micrometer divisions = 4 × 10 µm = 40 µm
Step 2: 50 epu = 40 µm, so 1 epu = 40 ÷ 50 = 0.8 µm
This calibration only applies to ×40. To use ×100 (oil immersion), recalibrate.
Magnification vs Resolution — the syllabus distinction
Candidates routinely confuse these terms. The syllabus requires defining each separately and explaining the difference — not just using them interchangeably.
| Term | Definition | What changes it |
|---|---|---|
| Magnification | How many times larger an image appears compared to the actual specimen | Lens system — can always be increased by adding lenses or projecting larger |
| Resolution | The minimum distance between two points at which they can still be distinguished as separate | Wavelength of the radiation used to view the specimen |
Electrons have a much shorter wavelength than visible light. Light microscopes have a resolution limit of about 200 nm — structures closer than this appear as one blur, no matter how high the magnification. Electron microscopes resolve to about 0.2 nm, revealing organelle ultrastructure.
Empty magnification: Increasing magnification beyond the resolution limit only makes the blur bigger — it adds no biological detail. This is why a light microscope at ×2000 shows nothing more than at ×1000.
Light vs Electron Microscopes
| Feature | Light microscope | Transmission EM (TEM) | Scanning EM (SEM) |
|---|---|---|---|
| Radiation | Visible light | Electron beam (transmitted) | Electron beam (reflected) |
| Maximum magnification | ~×1500 | ~×500 000 | ~×100 000 |
| Resolution | ~200 nm | ~0.2 nm | ~3–10 nm |
| Image type | Coloured (with stain) | 2D black & white | 3D-appearance black & white |
| Specimen state | Live or dead | Dead, dehydrated, in vacuum | Dead, dehydrated, in vacuum |
| Best for | Whole cells, tissues, processes | Internal organelle detail | Surface detail, 3D structure |
✕ "Electron microscopes magnify more, so they show more detail." — Wrong cause. They show more detail because of higher resolution, not magnification. A light microscope at ×2000 still has 200 nm resolution — just bigger blur.
✕ Confusing µm and nm in calculations — almost always loses the mark. Always state units in working.
✕ "Resolution" used to mean "image clarity" or "image sharpness" — the syllabus definition is specific: minimum separation distance.
Which statement correctly distinguishes resolution from magnification?
- A. Resolution can be increased indefinitely by adding more lenses.
- B. Magnification depends on the wavelength of radiation used.
- C. Resolution is the minimum distance between two points at which they can still be distinguished as separate.
- D. Light microscopes have higher magnification than electron microscopes.
A student observes a plant cell at ×400 magnification. The cell measures 32 eyepiece divisions across. Calibration showed that at ×400, 50 epu = 4 stage micrometer divisions, where each stage division is 10 µm.
(a) Calculate the value of 1 epu in µm. [2]
(b) Calculate the actual width of the cell in µm. [2]
(a) Value of 1 epu [2 marks]
4 stage divisions = 4 × 10 µm = 40 µm [1 mark for conversion]
1 epu = 40 µm ÷ 50 = 0.8 µm [1 mark for answer with unit]
(b) Actual cell width [2 marks]
Width = 32 epu × 0.8 µm [1 mark for setup]
= 25.6 µm [1 mark for answer with unit]
- Unit (µm) is required for full marks — bare number loses 1
- Working must show the calibration step explicitly; just stating "0.8 µm" without derivation typically scores half
- Answer 25.6 or 26 (sig fig dependent) both accepted
Cells as the basic units of living organisms
All living organisms are built of cells, and cells fall into two fundamentally different organisations: eukaryotic (with a true membrane-bound nucleus and complex organelles) and prokaryotic (without). Viruses are non-cellular — the syllabus uses them to challenge candidates to articulate what counts as life.
Eukaryotic cell organelles — structure and function
The syllabus expects candidates to recognise each organelle in photomicrographs and electron micrographs, and to outline its structure and function. Memorise the structure-function pairing for each:
| Organelle | Structure | Function | In plant? | In animal? |
|---|---|---|---|---|
| Nucleus | Surrounded by double membrane (nuclear envelope) with pores; contains chromatin and one or more nucleoli | Stores genetic information; controls cell activity through transcription | ✓ | ✓ |
| Nucleolus | Dense region within nucleus; not membrane-bound | Manufactures ribosomal RNA and assembles ribosomes | ✓ | ✓ |
| Rough ER (RER) | System of flattened membrane sacs (cisternae) studded with ribosomes | Synthesises and transports proteins (especially those for secretion) | ✓ | ✓ |
| Smooth ER (SER) | Membrane sacs without attached ribosomes | Synthesises lipids and steroids; detoxification | ✓ | ✓ |
| Golgi body | Stack of flattened membrane sacs (Golgi cisternae); vesicles bud from edges | Modifies, sorts, and packages proteins and lipids; produces glycoproteins; forms lysosomes | ✓ | ✓ |
| Ribosomes (80S) | Two subunits (large + small); not membrane-bound; ~25 nm | Site of protein synthesis (translation) | ✓ | ✓ |
| Mitochondrion | Double membrane; inner folded into cristae; matrix contains 70S ribosomes and circular DNA | Site of aerobic respiration; produces ATP | ✓ | ✓ |
| Lysosome | Single-membrane vesicle containing hydrolytic enzymes | Intracellular digestion; destruction of worn-out organelles (autophagy) | (rare) | ✓ |
| Centrioles | Pair of cylindrical bundles of microtubules at right angles | Organise microtubules during nuclear division (spindle formation) | − | ✓ |
| Microvilli | Finger-like extensions of cell surface membrane | Increase surface area for absorption (e.g. small intestine epithelium) | − | ✓ |
| Cilia | Hair-like projections; 9+2 arrangement of microtubules; basal body anchors | Beat to move fluid past cell surface (e.g. respiratory tract) | − | ✓ |
| Microtubules | Hollow tubes of tubulin protein; ~25 nm diameter | Cytoskeleton; organelle movement; spindle fibres; cilia/flagella core | ✓ | ✓ |
| Chloroplast | Double membrane; stroma contains stacks of thylakoids (grana); 70S ribosomes; circular DNA | Site of photosynthesis | ✓ | − |
| Permanent vacuole | Large central sac surrounded by the tonoplast (single membrane); contains cell sap | Maintains turgor; stores ions, sugars, pigments; some hydrolytic activity | ✓ | (small & temporary) |
| Cellulose cell wall | Rigid layer outside the cell surface membrane; cellulose microfibrils | Mechanical support; prevents cell bursting under turgor | ✓ | − |
| Plasmodesmata | Cytoplasmic strands through pores in adjacent plant cell walls | Allow movement of water, ions, and small molecules between cells | ✓ | − |
| Cell surface membrane | Phospholipid bilayer with embedded proteins; ~7 nm thick | Controls movement of substances; cell signalling; recognition | ✓ | ✓ |
The syllabus explicitly states (1.2 LO 4) that cells use ATP from respiration for energy-requiring processes. Examples to remember: active transport, protein synthesis, muscle contraction, DNA replication, mitosis, exocytosis. ATP itself is detailed in Topic 12 — here just connect "mitochondria → ATP → energy-requiring processes" as the chain.
Plant vs Animal cells — what differs
Plant and animal cells share most organelles. The syllabus expects candidates to compare structurally, focussing on what is present in one but not (or rarely) in the other:
| Feature | Plant cell | Animal cell |
|---|---|---|
| Cellulose cell wall | ✓ Always present, outside membrane | ✕ Absent |
| Chloroplasts | ✓ In photosynthetic cells | ✕ Absent |
| Permanent large vacuole | ✓ Central, fluid-filled, with tonoplast | Small, temporary vacuoles only |
| Plasmodesmata | ✓ Present | ✕ Absent |
| Centrioles | Generally absent | ✓ Present |
| Cilia / flagella (typical somatic cells) | Generally absent | In some cell types (e.g. respiratory epithelium) |
| Shape | Fixed by cell wall (often box-like) | Variable, often rounded |
| Storage carbohydrate | Starch grains | Glycogen granules |
✕ "Plant cells don't have mitochondria." — Wrong. All eukaryotic cells respire and need mitochondria. Photosynthesis produces glucose; respiration releases its energy.
✕ "Animal cells have no vacuoles." — Wrong. They have small, temporary vacuoles. The syllabus distinction is the permanent, large central vacuole, which is plant-specific.
✕ Lysosomes described as "plant organelles" because they sound similar to vacuoles — lysosomes are characteristic of animal cells.
Prokaryotic cells — the syllabus checklist
The 9700 syllabus (1.2 LO 5) gives an explicit list of features for "a typical bacterium". Memorise these six features:
Each prokaryote is a single cell. Some form colonies but each cell remains independent.
About 10× smaller than typical animal cells (~50 µm). Can be visualised under light microscope but ultrastructure requires EM.
A polymer of sugars cross-linked by short peptides. Different chemistry from cellulose (plant) or chitin (fungi). Targeted by penicillin (Topic 10).
One main circular chromosome floating freely in cytoplasm — not bounded by a membrane, so prokaryotes have no nucleus. Often plus small extra circular plasmids.
Smaller than 80S eukaryotic ribosomes. Same machinery for protein synthesis but different antibiotic sensitivity (e.g. streptomycin targets 70S).
No mitochondria, no chloroplasts, no nucleus. Some prokaryotes have internal membrane folds for respiration or photosynthesis, but no membrane-bound compartments.
Many antibiotics (streptomycin, tetracycline, erythromycin) target 70S ribosomes specifically. Because mitochondria and chloroplasts contain 70S ribosomes, prolonged high-dose antibiotic use can cause mitochondrial side effects — an evolutionary echo of the endosymbiotic origin of these organelles. (Topic 10 develops this.)
Prokaryote vs Eukaryote — comparison table
| Feature | Prokaryotic (bacterium) | Eukaryotic (plant / animal) |
|---|---|---|
| Typical size | 1–5 µm | 10–100 µm |
| Nucleus | ✕ Absent (DNA free in cytoplasm) | ✓ Membrane-bound nucleus |
| DNA arrangement | Circular chromosome (+ plasmids) | Linear chromosomes with histones |
| Ribosomes | 70S (smaller) | 80S (cytoplasm); 70S in mitochondria/chloroplasts |
| Cell wall | Peptidoglycan | Cellulose (plants); none (animals); chitin (fungi) |
| Membrane-bound organelles | ✕ None with double membrane | ✓ Mitochondria, chloroplasts, nucleus, etc. |
| Cell division | Binary fission | Mitosis or meiosis |
| Examples | E. coli, Mycobacterium tuberculosis | Onion epidermis, human epithelium |
Viruses — non-cellular structures
The syllabus carefully states (1.2 LO 7) that all viruses are non-cellular structures. A virus is not a cell — it has no cytoplasm, no ribosomes of its own, and cannot synthesise proteins or generate ATP outside a host cell. The syllabus expects candidates to know only three structural components:
Either DNA or RNA (but not both). Single- or double-stranded depending on the virus. Carries the genetic instructions for making more virus particles.
Protein shell surrounding the nucleic acid. Made of protein subunits (capsomeres) arranged in geometric patterns. Protects nucleic acid; provides surface proteins for host cell recognition.
Some viruses (e.g. HIV, influenza, SARS-CoV-2) have an outer envelope of phospholipids stolen from the host cell membrane during budding. Embedded glycoproteins help the virus bind to host receptors.
This is precisely why the syllabus places viruses in this topic — to make candidates think critically about the cell theory. Viruses replicate, evolve, and possess heritable information, but they cannot do so independently. They lack the metabolic machinery of cells. Most biologists treat them as biological entities at the boundary of life rather than as living organisms in the strict sense. A safe phrasing for exam answers: "Viruses possess some features of life such as heritable nucleic acid, but lack independent metabolism and reproduction, so they are conventionally regarded as non-cellular biological agents."
Which feature is found in a prokaryotic cell but NOT in a eukaryotic cell?
- A. A cell surface membrane
- B. Ribosomes
- C. A peptidoglycan cell wall
- D. Circular DNA in mitochondria
A student examines four structures under an electron microscope and lists their components. Which structure is a virus?
- A. Cell surface membrane, cytoplasm with 70S ribosomes, circular DNA, peptidoglycan wall
- B. Protein capsid surrounding RNA core, with phospholipid envelope and glycoprotein spikes
- C. Double membrane bounding stroma containing thylakoids, 70S ribosomes, and circular DNA
- D. Double membrane bounding cristae and matrix with 70S ribosomes and circular DNA
Compare the structure of a typical bacterium with that of a typical animal cell. Give THREE differences. [6]
Any three of the following differences (2 marks each — 1 for the bacterial feature, 1 for the contrasting animal feature):
- DNA arrangement: bacterium has circular DNA free in cytoplasm; animal cell has linear chromosomes inside a membrane-bound nucleus
- Ribosomes: bacterium has 70S ribosomes only; animal cell has 80S ribosomes (plus 70S in mitochondria)
- Cell wall: bacterium has a peptidoglycan cell wall; animal cell has no cell wall
- Membrane-bound organelles: bacterium has none with double membranes; animal cell has nucleus, mitochondria, etc.
- Size: bacterium is 1–5 µm; animal cell is typically 10–100 µm
- Cell division: bacterium divides by binary fission; animal cell by mitosis
Mark scheme guidance: Each comparison must explicitly contrast both organisms — just stating "bacteria are smaller" without naming the animal cell scale typically scores 1 of 2. Use comparative connectives ("whereas", "in contrast", "but").
Topic 1 Practice — Comprehensive
Mixed practice in 9700 P1/P2 style. Cover the answer; attempt fully; check; record where the rubric points are won or lost.
A bacterial cell appears 12 mm long on an electron micrograph stated as ×6000. The actual length of the cell is
- A. 0.2 µm
- B. 2.0 µm
- C. 20 µm
- D. 200 µm
Image size 12 mm = 12 000 µm. Actual size = 12 000 ÷ 6000 = 2.0 µm. Sense check: typical bacteria are 1–5 µm, so 2.0 is plausible. (A) miscalculates; (C) forgets to convert mm; (D) is in the wrong order of magnitude.
An electron micrograph shows a cell with: a true nucleus surrounded by a double membrane, mitochondria with cristae, chloroplasts containing grana, and a large central vacuole bounded by a single membrane. The cell is
- A. an animal cell
- B. a plant cell
- C. a bacterial cell
- D. a virus
Two ribosomes lie 20 nm apart in a cell. Which microscope can distinguish them as separate structures?
- A. Light microscope at ×1000
- B. Light microscope at ×3000 with oil immersion
- C. Transmission electron microscope
- D. None — ribosomes cannot be visualised
Fig. 1 (not shown) is an electron micrograph of a single cell, magnification ×15 000.
(a) The cell shows a double-membrane bounded structure containing folded inner membranes (cristae) and a 70S ribosome. Identify this organelle and state TWO functions of the inner membrane folding. [3]
(b) The cell also contains chloroplasts. State TWO conclusions you can reach about this cell's identity, and justify each. [3]
(c) On Fig. 1, the cell measures 90 mm across at the widest point. Calculate the actual diameter of the cell in µm. [2]
(a) Mitochondrion + cristae function [3 marks]
Organelle: mitochondrion [1]
Two functions of inner membrane folding (cristae):
- Increases surface area for the embedded electron transport chain proteins / ATP synthase — allowing more ATP production per mitochondrion [1]
- Compartmentalises the intermembrane space from the matrix, enabling the proton gradient required for chemiosmosis [1]
(b) Cell identity from chloroplasts [3 marks]
Conclusion 1: The cell is eukaryotic [1]
Justification: chloroplasts are double-membrane organelles, only present in eukaryotic cells (prokaryotes have no double-membrane organelles) [1]
Conclusion 2: The cell is from a plant (or photosynthetic protoctist) [1]
Justification: chloroplasts are restricted to photosynthetic eukaryotes; animal cells do not contain them.
(c) Actual diameter [2 marks]
Image size: 90 mm = 90 000 µm [1 for unit conversion]
Actual size = 90 000 µm ÷ 15 000 = 6.0 µm [1 for answer with unit]
- (a) "More surface area for ATP production" alone scores 1 only. The question asks for TWO functions — chemiosmosis/proton gradient is the second mark
- (b) Stating "plant cell" without justification scores at most 1 of 2 conclusions. Justify means link the structural feature to the inference
- (c) Bare numerical answer "6.0" without µm scores half — units always count
Topic 1 — Common Mistakes
- 🔭Confusing magnification with resolutionMagnification = how many times bigger the image is. Resolution = minimum separation that can still appear as two points. Boosting magnification beyond the resolution limit produces empty magnification — a bigger blur.
- 📏Forgetting unit conversion before dividingImage size in mm and actual size in µm must be in the same unit. Standard P3 calculation losing pattern: 28 mm ÷ 14 000 (correct number) but in mm gives 0.002 mm — correct numerically but wrong unit means lost mark.
- 🔬Saying plant cells lack mitochondriaAll eukaryotic cells respire, including plants. Mitochondria are present in every plant cell. Photosynthesis fixes carbon in chloroplasts; respiration releases its energy in mitochondria.
- 🧹Saying animal cells lack vacuolesThey have small, temporary vacuoles. The plant-specific feature is the large permanent central vacuole bounded by the tonoplast. Be precise.
- 🧬Confusing ribosome typesProkaryotes have 70S only. Eukaryotic cytoplasm has 80S. But mitochondria and chloroplasts contain 70S — an evolutionary echo of endosymbiosis. Saying "eukaryotes have 80S ribosomes" is incomplete.
- 🧐Treating viruses as a third type of cellViruses are non-cellular structures. They have no cell membrane, no cytoplasm, no ribosomes of their own. The syllabus is precise on this and so should answers be.
- 🔌"Resolution increases with magnification"Wrong direction of causation. Resolution depends on the wavelength of the radiation used — not on magnification or lens count. Adding lenses can only magnify what is already resolved.
- 🍁Mixing up cell wall chemistry across kingdomsPlants = cellulose. Bacteria = peptidoglycan. Fungi = chitin. Animals = no cell wall. The 9700 syllabus only requires plant (cellulose) and bacterial (peptidoglycan), but the chitin/animal contrasts often appear in distractor options.
- ❓Listing organelles without describing structureThe syllabus verb is "outline structures and functions". Just naming a function (e.g. "mitochondria make ATP") loses marks for missing structural features (double membrane, cristae, matrix). Always pair structure with function.
- ✏Drawing rule violationsSketchy multiple lines, shading, arrows for labels, missing scale bar, drawing what's expected rather than visible — all standard P3 deductions. Always single clean lines, horizontal label lines, scale bar OR magnification (not both).
Topic 1 underpins Topics 4 (membranes), 5 (mitosis), 6 (nucleic acids), 7 (transport in plants), and 11 (immunity). The highest-value items to over-prepare are: magnification calculations with unit conversion, the prokaryote 6-feature checklist, the plant-vs-animal comparison table, and the resolution-vs-magnification distinction. These appear in some form in nearly every Paper 1 series and are frequently embedded in Paper 2 structured questions on tissues from later topics.