3.2.1 Cell structure

Cell structure is the inventory. Eukaryotic cells with their compartmentalised organelles, prokaryotic cells with no nucleus and no membrane-bound compartments, viruses that are not cells at all. Plus the two techniques that reveal the system: microscopy and cell fractionation.

Eukaryotic cells run on a system of membrane-bound organelles.

The defining feature of a eukaryotic cell is compartmentalisation. A membrane-bound nucleus sits at the centre; an array of additional membrane-bound organelles handles the rest. Each compartment runs its own biochemistry at its own pH, with its own enzymes, separated from the cytoplasm by membranes. Incompatible reactions run simultaneously without colliding.

Write ATP, not energy, for mitochondrial function. "Mitochondria produce energy" is an explicit reject. The credit term is ATP, produced through aerobic respiration.

Ribosomes are made of rRNA and protein — not DNA, not tRNA, not mRNA. On a 2017 1-mark composition question, the majority of students wrote one of the rejected nucleic acids. The composition is rRNA and protein; nothing else scores.

Prokaryotic cells are simpler — no nucleus, no membrane-bound organelles.

Prokaryotes (bacteria, in AQA scope) are structurally simpler and substantially smaller. No nucleus; the genome is a single circular DNA chromosome in the nucleoid, not associated with histones. No membrane-bound organelles. Smaller (70S) ribosomes, a murein cell wall, and mesosomes — infoldings of the inner membrane associated with respiration.

Murein is the bacterial cell-wall polymer; chitin is the fungal one; cellulose is the plant one. Swapping murein and chitin, or assigning either to plants, is a documented mark-scheme error. The three-way pairing is tested directly.

Pitfall — The list rule

The list rule — "all prokaryote" questions are not "features that differ from eukaryotes".

When a question asks for a feature found in all prokaryotic cells, build the answer from universally true features only. Plasmid, capsule, flagellum: none is in every prokaryote. 70S ribosomes are present in all prokaryotes, but also in eukaryotic mitochondria and chloroplasts, so they are not prokaryote-exclusive. One non-universal item in the list collapses the whole answer to zero. On the 2022 1-mark "feature in ALL prokaryotes" question, only one in five students scored.

Viruses are acellular and non-living — capsid, genetic material, attachment proteins.

Viruses are not cells and not alive. They lack cellular structure, lack metabolism, and can only replicate inside a host cell using the host's machinery. Two separate parallel definitions describe these properties: acellular (structural) and non-living (functional). The two are marked independently.

Capsid is the protein coat of a virus. Capsule is the polysaccharide coat on some prokaryotes. Different structures, different organisms; the names are easily confused. Write the right one for the right organism.

Microscopy: resolution sets the limit, not magnification.

Resolution is the minimum distance at which two objects can still be distinguished as separate. It is limited by the wavelength of the radiation used; shorter wavelengths give finer resolution. Magnification is image size relative to actual size. The two are not interchangeable. When an optical microscope cannot show a small organelle, the reason is insufficient resolution.

When the optical microscope can't show a structure, the answer is resolution — not magnification and not clearer. "Greater resolving power" and "more detail" earn the mark. "Clearer" or "better magnification" do not.

Compare-and-contrast questions need paired statements. "TEM uses electrons, optical uses light" scores; "TEM uses electrons" followed separately by "optical uses light" does not. On 2017 P1 Q10.1 (a 6-mark comparison), the dominant failure was parallel description instead of paired contrast.

Cell fractionation: cold, isotonic, buffered, then graded centrifugation.

Cell fractionation separates organelles from cells so their composition and function can be studied. Four sequential steps, each independently credited. The most consistently dropped mark across the cohort is the conditions of the homogenisation solution.

1. Homogenise the tissue by mechanical disruption (blender or homogeniser) in a cold, isotonic, buffered solution to release the organelles intact.
2. Filter the homogenate to remove cell debris and large unbroken fragments.
3. Centrifuge at a low speed first. The densest organelles, the nuclei, pellet at the bottom; the supernatant is transferred to a fresh tube.
4. Centrifuge at progressively higher speeds. Mitochondria pellet at intermediate speeds; lysosomes and ribosomes at higher speeds. Each successive supernatant is re-spun.

All three conditions — cold, isotonic, buffered — must be named. Naming two scores at most two-thirds. "Same water potential" is an accepted variant for isotonic; "pH controlled" is accepted for buffered.

Low speed first, then progressively higher. "Spin faster" or "high speed only" loses the slow-first principle mark. The order of speeds is the mark point, not just the act of centrifuging.

Pitfall — Differential vs ultracentrifugation

Standard differential centrifugation isolates organelles. Ultracentrifugation isolates molecules.

Differential centrifugation pellets organelles in order of mass — nuclei first, then mitochondria, then smaller organelles — at progressively higher speeds. Ultracentrifugation runs at very high speeds and is used to separate molecules (e.g. proteins) from the supernatant after all organelles have been pelleted out. Describing standard differential centrifugation when the question asks about molecule isolation is a documented error: 2018 P3 Q05.2 ran at 7% mastery; 2024 P1 Q10.1 carried a high-tariff penalty for the same conflation.

Key terms

• ribosomes
• mitochondria
• prokaryotic
• cell wall
• capsid
• acellular
• non-living
• resolution
• magnification
• organelle
• centrifuge
• pellet