Cell Structure

AQA spec ref: 3.2.1 - Prokaryotic and eukaryotic cells; 3.2.2 - All cells arise from other cells

All living cells fall into one of two fundamental categories: prokaryotic (bacteria and archaea) or eukaryotic (all other organisms - plants, animals, fungi, protists). The distinction between these is arguably the most important division in all of biology. Eukaryotic cells are more complex, larger, and compartmentalised into organelles - each organelle is adapted for a specific function. Understanding cell structure requires knowing not just what each organelle does, but why its structure makes it suited to that function.

The Prokaryote - Eukaryote Divide

The prokaryote - eukaryote divide

Everything alive is either prokaryotic or eukaryotic, and this is one of the most important distinctions in biology. Prokaryotic cells have no membrane-bound nucleus. Their DNA floats freely in the cytoplasm as a single, circular chromosome. Eukaryotes, by contrast, have their DNA enclosed within a double-membrane nucleus, and their cells are compartmentalised into distinct organelles, each doing a specific job.

Distinctions

Prokaryotes are considerably smaller - typically 1 - 10 µm compared to 10 - 100 µm for eukaryotic cells.
The cell wall is made of murein (a peptidoglycan), not cellulose (which is what plant cell walls are made of)
Prokaryotes also have plasmids - small, circular loops of DNA separate from the main chromosome, often carrying antibiotic resistance genes
Many prokaryotes have a capsule (a layer of polysaccharide outside the cell wall) for protection and adhesion
pili (protein filaments used for attachment and conjugation), and flagella for movement - though prokaryotic flagella are structurally completely different from eukaryotic flagella.

Eukaryote Structure

Nucleus

Houses cells genetic material, its outer boundary is the nuclear envelope - a double phospholipid bilayer. This double membrane is continuous with the rough endoplasmic reticulum, which is important: it means newly made proteins can be threaded directly into the ER lumen without being exposed to the cytoplasm.

The nuclear envelope is perforated by nuclear pores - large protein complexes roughly 120 nm in diameter. These are not just holes; they are highly selective gatekeepers that control the passage of molecules in and out. mRNA exits through them (heading to ribosomes), and transcription factors, RNA polymerase, and nucleotides enter through them. Pore number correlates with transcriptional activity - cells that are synthesising a lot of protein have more nuclear pores.

Mitochondria

Mitochondria are the sites of aerobic respiration, and their structure is exquisitely adapted for this role. Each mitochondrion has a double membrane - an outer membrane that is relatively smooth and permeable, and an inner membrane that is highly folded into projections called cristae. These folds massively increase the surface area of the inner membrane, which is where the electron transport chain (ETC) and ATP synthase enzymes are embedded. More cristae = more surface area for oxidative phosphorylation = more ATP.

The space enclosed by the inner membrane is the matrix, which contains the enzymes of the Krebs cycle, mitochondrial ribosomes (70S - same size as bacterial ribosomes), and a small circular loop of mitochondrial DNA. The presence of 70S ribosomes and circular DNA is the basis of the endosymbiotic theory - the idea that mitochondria evolved from a free-living proteobacterium that was engulfed by a larger cell. This is why mitochondria can self-replicate by binary fission, independently of the cell cycle.

Cells with high energy demands - like muscle cells, sperm cells (in the midpiece), and intestinal epithelial cells - have proportionally more mitochondria and more densely packed cristae.

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Ribosomes

Ribosomes are the molecular machines that translate mRNA into protein (see DNA replication and Protein synthesis). They are not membrane-bound - they are simply protein-rRNA complexes. Eukaryotic ribosomes are 80S (made of a 60S large subunit and a 40S small subunit). They are found either free in the cytoplasm (making proteins for use inside the cell) or attached to the rough ER (making proteins destined for secretion or insertion into membranes).

The 70S vs 80S distinction is not just trivial biochemistry - it is the target of antibiotics such as streptomycin and tetracycline, which interfere with 70S ribosome function without affecting 80S ribosomes. Understanding why this difference matters shows the examiner you actually understand the concept rather than just memorising numbers.

The Endomembrane System: Rough ER → Golgi → Vesicle

The rough ER, smooth ER, and Golgi form a continuous system for making, modifying, and dispatching proteins and lipids. Understanding the sequence is important for exam questions.

The rough ER is studded with ribosomes (giving its rough appearance under the EM). Proteins synthesised on these ribosomes are threaded co-translationally into the lumen of the ER, where they undergo initial folding and modification (including the addition of oligosaccharide chains - glycosylation). They are then packaged into transport vesicles that bud off the ER membrane and travel to the Golgi.

The Golgi apparatus is a stack of flattened membrane sacs called cisternae. Vesicles arrive at the cis face (facing the ER) and leave from the trans face. As proteins move through the Golgi, they are further processed - the sugar chains added in the ER are trimmed and modified, signal sequences are added to direct proteins to their final destinations, and proteins are sorted into different vesicles depending on whether they are heading to lysosomes, the plasma membrane, or secretion outside the cell.

The smooth ER has no ribosomes and is involved in lipid and steroid synthesis, detoxification (particularly in liver cells), and calcium ion storage (in muscle cells, where calcium release triggers contraction).

Lysosomes

Lysosomes are membrane-bound organelles containing around 50 different hydrolytic enzymes (including proteases, lipases, DNases, and glycosidases) that work optimally at pH 5 - which is why the lysosomal lumen is kept acidic. The acid pH is maintained by proton pumps in the lysosomal membrane, and it is also a safety mechanism: if a lysosome ruptures and spills its contents into the neutral cytoplasm (pH ~7.2), the enzymes are largely inactivated.

Their roles include digesting material brought in by endocytosis (including pathogens ingested by white blood cells), breaking down worn-out organelles (autophagy), and programmed cell death (apoptosis), where lysosomal enzymes are deliberately released to dismantle the cell from within.

Centrioles

Centrioles are found in animal cells (and some lower plant cells), but not in higher plant cells - a distinction the exam loves to test. They consist of nine triplets of microtubules arranged in a ring, and they form the mitotic spindle during cell division. They are found in pairs at right angles to each other, forming the centrosome, which organises the spindle fibres that pull chromosomes to opposite poles during mitosis and meiosis.

Plant cells - the additional structures

Plant cells have three structures that animal cells lack:

The cell wall is made of cellulose microfibrils - long, unbranched chains of β-glucose linked by β-1,4 glycosidic bonds, forming strong hydrogen-bonded bundles. The cell wall provides structural support and prevents osmotic lysis (the cell wall resists the expansion caused by water entering by osmosis, creating turgor pressure). It is fully permeable to water and small solutes.

The large permanent vacuole is surrounded by the tonoplast (a selectively permeable membrane) and filled with cell sap - a solution of salts, sugars, and organic acids. It maintains turgor, stores pigments (like anthocyanins in red/purple plants), and can store waste products.

Chloroplasts are found in photosynthetic plant cells. Like mitochondria, they have a double membrane - but inside they also have an elaborate third membrane system: a network of flattened membrane sacs called thylakoids, stacked into columns called grana (singular: granum), connected by lamellae. The thylakoid membranes are where the light-dependent reactions of photosynthesis occur (they carry chlorophyll and other photosynthetic pigments, as well as the electron transport chain and ATP synthase). The fluid-filled space surrounding the thylakoids - the stroma - is where the light-independent reactions (Calvin cycle) take place. Like mitochondria, chloroplasts contain 70S ribosomes and circular DNA, again supporting the endosymbiotic theory.

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Summary

Prokaryote vs eukaryote: prokaryotes have no membrane-bound nucleus, circular DNA, no membrane-bound organelles, murein cell wall, 70S ribosomes, 1 - 10 µm. Eukaryotes have a nuclear envelope, linear chromosomes on histones, membrane-bound organelles, 80S ribosomes, 10 - 100 µm.
Nucleus: double membrane (nuclear envelope), nuclear pores control traffic, contains chromatin (DNA + histones)
Mitochondria: double membrane, inner membrane folded into cristae (site of ETC + ATP synthase), matrix (Krebs cycle enzymes + 70S ribosomes + circular DNA)
Ribosomes: 80S in eukaryotes (60S + 40S subunits); 70S in prokaryotes and organelles. Free = cytoplasmic proteins; rough ER-bound = secretory proteins
Rough ER → Golgi → vesicle: protein synthesis on rough ER → transport vesicles → Golgi (processing/sorting) → secretory vesicles
Lysosomes: hydrolytic enzymes at pH 5; digest engulfed material, worn organelles (autophagy), apoptosis
Centrioles: in animal cells only; form mitotic spindle; nine triplets of microtubules
Plant-only structures: cell wall (cellulose microfibrils, β-1,4 linkages), permanent vacuole (tonoplast membrane), chloroplasts (thylakoids/grana for light reactions; stroma for Calvin cycle)
Endosymbiotic theory: mitochondria and chloroplasts have 70S ribosomes and circular DNA→descended from engulfed bacteria

AQA Exam Tips

Prokaryote definition: "has no membrane-bound nucleus" - not just "has no nucleus." Prokaryotes do have DNA; it's just not enclosed in a nucleus.
Murein vs cellulose: prokaryote cell walls = murein (peptidoglycan). Plant cell walls = cellulose. AQA tests this distinction. Do not say bacteria have cellulose walls.
70S vs 80S ribosomes: this matters for antibiotics - drugs like streptomycin target 70S ribosomes (bacteria) without affecting 80S ribosomes (eukaryotic cells). Explains selective toxicity.
Why cells need many mitochondria: cells with high energy demand (muscle, liver, sperm midpiece) need more ATP → more mitochondria. The AQA question is usually "suggest why this cell has many mitochondria" - answer: high rate of aerobic respiration to produce ATP for [specific activity].
Golgi apparatus function: modify and sort proteins for secretion, insertion into membranes, or delivery to lysosomes. Always say "modifies" not just "packages."
Endosymbiotic evidence: 70S ribosomes (same as bacteria), own circular DNA, divide by binary fission independently of the cell cycle. State all three for a full-mark answer.
Scale and units: organelles are measured in nanometres (nm) and micrometres (µm). Know approximate sizes: ribosome ~20 nm, mitochondrion ~1 - 10 µm, nucleus ~5 - 10 µm.