Cell structure
🎯What you need to be able to do
- State cell theory and use it to make a prediction about a newly discovered organism.
- Use a light microscope: make temporary mounts, stain, focus, measure with an eyepiece graticule, and calculate magnification, actual size and scale bars.
- Outline the advantages of electron microscopy, freeze fracture, cryogenic electron microscopy, fluorescent stains and immunofluorescence.
- Describe the structures common to all cells and explain why each is needed.
- Describe the structure of a prokaryote cell and of a typical eukaryote cell.
- List the functions of life in a unicellular organism.
- Compare animal, plant and fungal cells, and explain the atypical structure of hyphae, muscle fibres, red blood cells and sieve tube elements.
- Identify cells and structures in light and electron micrographs, and draw and annotate them with functions.
- AHL Explain the evidence for endosymbiosis, the basis of cell differentiation, and the evolution and advantages of multicellularity.
📚The biology
Cell theory
Cell theory states that cells are the basic structural unit of all living organisms: every organism is made of one or more cells, and nothing smaller than a cell is alive on its own. It is one of the best-supported generalizations in biology, and it allows deductive reasoning: if a new organism is discovered, we can predict before examining it that it will be made of cells.
Microscopy skills
You are expected to have used a light microscope, not just read about one. The core skills:
- Temporary mounts. Place a thin layer of tissue (onion epidermis, cheek cells, a leaf peel) in a drop of water or stain on a slide, and lower a cover slip at an angle to avoid trapping air bubbles.
- Staining. Most cell contents are transparent. Stains such as iodine (starch, nuclei in plant cells) or methylene blue (nuclei in animal cells) increase contrast.
- Focusing. Start on the lowest-power objective. Use the coarse focus only at low power; use the fine focus at high power, where the coarse knob could crash the lens into the slide.
- Measuring. An eyepiece graticule is a scale in the eyepiece with no units. Calibrate it for each objective against a stage micrometer (a slide with a scale of known length), then use it to measure cells.
- Photographs can be taken through the eyepiece or with a camera attachment, and measured afterwards.
Measuring with a graticule is quantitative observation: the instrument turns a visual impression into a number with a known precision.
Magnification, actual size and scale bars
Every calculation uses one relationship:
Rearrange it for whichever quantity is unknown. The units of image size and actual size must be the same before you divide.
1 mm = 1000 µm
1 µm = 1000 nm
eukaryote cell 10–100 µm
prokaryote cell 1–5 µm
virus 20–300 nm
A line on an image labelled with the actual length it represents. Measure the bar and use its label to find the magnification.
The prefixes kilo, centi, milli, micro and nano are defined by international agreement, which is why a micrometre means the same thing in every laboratory in the world.
Developments in microscopy
Uses beams of electrons, which have a much shorter wavelength than light. The resolution is far higher (about 0.2 nm against 200 nm), revealing ribosomes, membranes and the internal structure of organelles. Specimens must be dead and in a vacuum.
A specimen is frozen rapidly and cracked. The fracture tends to split membranes down the middle of the bilayer, showing proteins embedded in the membrane — key evidence for the fluid mosaic model.
Specimens are frozen so fast that water forms glass-like ice rather than crystals, preserving molecules close to their natural state. Images of many molecules are combined to find the 3D structure of individual proteins.
Dyes that bind specific substances (for example DNA) and glow when illuminated with particular wavelengths, used in light microscopy to show where a substance is located, even in living cells.
Antibodies that bind one specific protein are tagged with a fluorescent dye, so that only that protein lights up. Several proteins can be shown at once in different colours.
Structures common to all cells
Every typical cell, prokaryote or eukaryote, has three things, and each has a reason:
- DNA as genetic material — the instructions for making the cell’s proteins, which can be copied and passed on when the cell divides.
- Cytoplasm, composed mainly of water — the medium in which enzymes and substrates are dissolved and metabolic reactions happen.
- A plasma membrane made mainly of lipids — a barrier that keeps the cytoplasm in and controls what enters and leaves, so conditions inside can differ from outside.
Prokaryote cells
Prokaryotes lack a nucleus and membrane-bound organelles. The syllabus uses the structure of Gram-positive eubacteria such as Bacillus and Staphylococcus:
Outside the membrane; made of peptidoglycan. Resists bursting when water enters by osmosis.
Controls entry and exit of substances.
No compartments; contains enzymes and all metabolic reactions.
A single circular chromosome, not associated with histones, in a region called the nucleoid.
Smaller than eukaryote ribosomes; site of protein synthesis.
Prokaryote structure varies considerably — some have flagella, pili, plasmids, a capsule or no cell wall at all — but you are only required to know the structure above.
Eukaryote cells
A eukaryote cell has a plasma membrane enclosing a compartmentalized cytoplasm. Its common features:
- 80S ribosomes, larger than those of prokaryotes.
- A nucleus surrounded by a double membrane with pores, containing chromosomes made of linear DNA bound to histone proteins.
- Mitochondria, the site of aerobic respiration.
- Endoplasmic reticulum: rough ER, with ribosomes, synthesizes proteins for secretion; smooth ER synthesizes lipids.
- Golgi apparatus, which processes proteins and packages them into vesicles.
- Vesicles and vacuoles, including lysosomes, which contain digestive enzymes.
- A cytoskeleton of microtubules and microfilaments, which supports the cell, gives it shape, and moves organelles and chromosomes.
Life processes in unicellular organisms
A unicellular organism such as Paramecium or Chlamydomonas must carry out every function of life within one cell:
keeping internal conditions within limits (e.g. contractile vacuoles expel excess water)
all the chemical reactions of the cell
obtaining food, by photosynthesis or by feeding
e.g. using cilia or a flagellum
removing waste products of metabolism
an increase in size and mass
e.g. moving towards light
producing offspring, sexually or asexually
Animal, fungal and plant cells compared
Plant: yes, of cellulose
Fungus: yes, of chitin
Animal: none
Plant: a large permanent sap vacuole, keeping the cell turgid
Fungus: may have large vacuoles
Animal: small, temporary vacuoles (e.g. food vacuoles in phagocytes)
Plant: chloroplasts in green tissues; other plastids such as amyloplasts store starch
Fungus and animal: none
Animal: present
Plant and most fungi: absent
Animal: many cells, e.g. sperm, airway lining
Plant: absent in flowering plants
Fungus: mostly absent
Atypical eukaryote cells
A “typical” eukaryote cell has one nucleus. Several important cells do not, and each is atypical for a reason:
Many nuclei. The hyphae have no cross-walls (septa), so the cytoplasm forms one long continuous tube with nuclei spread along it.
Many nuclei. Each fibre forms by the fusion of many cells, giving a single very long structure that can contract as a unit.
No nucleus in mammals. The nucleus is lost as the cell matures, leaving more space for haemoglobin.
No nucleus and few organelles, leaving an open channel for sap to flow; a companion cell alongside keeps them alive.
Micrographs: identifying and drawing
You must be able to decide whether a cell in a micrograph is prokaryote, plant or animal. The deciding features: a prokaryote is small, with no nucleus and no membrane-bound organelles; a plant cell has a cell wall, usually a large vacuole and often chloroplasts; an animal cell has no wall, no large vacuole and an irregular shape.
In electron micrographs you should recognize the nucleoid region, prokaryotic cell wall, nucleus, mitochondrion, chloroplast, sap vacuole, Golgi apparatus, rough and smooth ER, chromosomes, ribosomes, cell wall, plasma membrane and microvilli. Some recognition cues:
- Mitochondrion: oval, double membrane, inner membrane folded into cristae.
- Chloroplast: larger, double membrane, stacks of flattened thylakoids (grana).
- Golgi apparatus: a stack of curved, flattened sacs with vesicles budding from the edges; no ribosomes.
- Rough ER: parallel flattened sacs dotted with dark ribosomes. Smooth ER: tubular, no ribosomes.
- Microvilli: finger-like projections of the plasma membrane, increasing surface area.
When you draw and annotate, use clear single lines, no shading, label lines that do not cross, and add a function to each label — the syllabus requires annotations, not just names. For example: rough ER — synthesizes proteins for secretion.
The origin of eukaryote cells by endosymbiosis AHL
The evidence suggests that all eukaryotes evolved from a common unicellular ancestor that already had a nucleus and reproduced sexually. Mitochondria then arose by endosymbiosis: an aerobic prokaryote was taken in by this cell but not digested, and lived inside it, supplying ATP in exchange for protection and nutrients. Over time the two became completely interdependent. Later, in the lineage leading to plants and algae, chloroplasts arose in the same way from an engulfed photosynthetic prokaryote.
The evidence that mitochondria and chloroplasts were once free-living prokaryotes:
- they contain 70S ribosomes, like prokaryotes, not the 80S ribosomes of the surrounding cytoplasm;
- they have their own naked, circular DNA, like prokaryotes;
- they replicate by dividing, like bacteria, and cannot be made by the cell from scratch;
- they have a double membrane, consistent with an engulfed cell inside a vesicle.
A theory is strong when it accounts for many independent observations and its predictions keep being supported. Endosymbiosis explains all of these at once, and later gene sequencing confirmed its prediction that mitochondrial DNA is most similar to that of a particular group of bacteria.
Cell differentiation AHL
In a multicellular organism, all body cells carry the same genes, yet they develop into very different specialized cells. The basis of differentiation is different patterns of gene expression: each cell type switches on some genes and switches off others. Changes in a cell’s environment — signals from neighbouring cells, the concentration of a chemical in the embryo — often trigger these changes (B2.3, D2.2).
The evolution of multicellularity AHL
Multicellularity has evolved many times independently: many fungi and eukaryotic algae are multicellular, and all plants and all animals are. It evolved repeatedly because it brings advantages:
- Larger body size, which can help avoid predators, compete for light, or catch larger prey.
- Cell specialization: different cells can become adapted to different functions, so that each is carried out more efficiently than a single cell doing everything.
✏️Worked example
(b) A scale bar on a light micrograph is 25 mm long and labelled 10 µm. Calculate the magnification of the micrograph.
(c) Using a ×40 objective, 40 eyepiece graticule units line up with 10 divisions of a stage micrometer. Each stage micrometer division is 10 µm. A cheek cell is 18 eyepiece units across. Calculate its diameter.
(a) Convert the image size to micrometres first: 24 mm = 24 000 µm.
(b) The scale bar is an image of a known actual length. Convert: 25 mm = 25 000 µm.
(c) First calibrate the graticule. Ten stage divisions are 10 × 10 = 100 µm, and this matches 40 eyepiece units:
Then the cell: 18 × 2.5 = 45 µm.
📝Practise
Work through these on paper, then reveal the answer. Question 6 is AHL.
1. A bacterium is 2 µm long. In a micrograph its image is 16 mm long. Calculate the magnification.
2. State the structures you would expect to find in a Gram-positive bacterium, and one structure found in all eukaryotes but in no prokaryote.
3. Compare the cell walls and vacuoles of plant, fungal and animal cells.
4. Explain why a skeletal muscle fibre and a red blood cell are both described as atypical.
5. Outline two advantages of electron microscopes over light microscopes, and one advantage of light microscopes.
6. AHL Outline the evidence that mitochondria evolved from free-living prokaryotes.
🔗Go deeper — other people’s work
These are external resources, not mine. If one stops working, tell me and everything above it on this page still stands.
- The Cell Image Library — a free collection of real light and electron micrographs, good for practising identification of organelles.
- Learn.Genetics (University of Utah), Cell Size and Scale — an interactive zoom from a coffee bean down to a carbon atom that makes the units stick.
- Nikon MicroscopyU and Zeiss Microscopy education pages — clear explanations of fluorescence and immunofluorescence with example images.