Eukaryotic Cell Structure and Organelles — AQA A-level Biology

SPEC 3.2.1.1 - CELLS

Eukaryotic Cell Structure

Organelles, their ultrastructure and functions — and how to explain cell adaptations for full marks

The Eukaryotic Cell

All animals, plants, fungi and protoctists are made of eukaryotic cells. The defining feature is how it is organised.

DEFINITION

Eukaryotic cell: A cell that contains a membrane-bound nucleus and membrane-bound organelles, in which the genetic material is linear DNA associated with histone proteins, forming chromosomes.

DEFINITION

Organelle: A discrete, membrane-bound structure within a cell that performs a specific function.

Why Compartmentalisation Matters

The membrane around each organelle creates a separate internal environment, allowing different biochemical reactions to occur simultaneously without interfering with each other. This compartmentalisation is the key advantage of eukaryotic organisation.

The Nucleus

The nucleus is the largest organelle and the control centre of the cell. Every structural feature has a functional explanation.

Structure

Nuclear envelope — double membrane

Nuclear pores — allow mRNA and ribosomal subunits to exit

Chromatin = DNA wound around histone proteins

Nucleolus = site of rRNA synthesis and ribosome assembly

Function

Contains and protects genetic information

Controls gene expression — which proteins are synthesised

Nuclear pores export mRNA to cytoplasmic ribosomes for translation

Mitochondria

Site of aerobic respiration. Complex internal structure directly maximises ATP production.

FeatureStructureFunctional Significance

Outer membraneSmooth phospholipid bilayerControls entry/exit of substances

Inner membrane (cristae)Highly folded inward projectionsIncreases surface area for ATP synthase; site of oxidative phosphorylation

MatrixFluid; circular DNA; 70S ribosomes; enzymesSite of Krebs cycle; self-replication supports endosymbiotic theory

Examiner Alert

Never write "cristae provide more room." Say: cristae increase the surface area for ATP synthase proteins, maximising ATP production by oxidative phosphorylation. The words "surface area" are required for the mark.

Chloroplast (Plants & Algae)

Site of photosynthesis. Two distinct internal regions carry out the two stages.

Grana (Thylakoid Stacks)

Stacked disc membranes containing chlorophyll. Site of the light-dependent reaction — absorbs light, splits water (photolysis), produces ATP and reduced NADP. Large SA for light absorption.

Stroma

Fluid matrix surrounding grana. Contains enzymes (RuBisCO), circular DNA, 70S ribosomes, starch granules. Site of the light-independent reaction (Calvin cycle) — CO₂ fixation into organic molecules.

Endoplasmic Reticulum & Ribosomes

ROUGH ER (RER)

Membrane-bound cisternae (flattened sacs) studded with ribosomes. Continuous with the outer nuclear envelope. Synthesises and transports secretory proteins into the RER lumen toward the Golgi.

SMOOTH ER (SER)

Cisternae without ribosomes. Synthesises lipids and steroid hormones; detoxification in liver cells (e.g. breaks down alcohol and drugs).

RIBOSOMES

Composed of ribosomal RNA and protein. Two subunits. Not membrane-bound.TypeSizeWhereEukaryotic80SCytoplasm; on RERProkaryotic70SCytoplasmOrganellar70SMitochondria; chloroplasts

Synoptic Link

70S ribosomes in mitochondria and chloroplasts are key evidence for the endosymbiotic theory. Can appear in Paper 3 evolution essays.

Golgi Apparatus & Lysosomes

Golgi Apparatus

Receives transport vesicles from RER (cis face)

Modifies proteins: glycosylation (adds carbohydrate chains to form glycoproteins)

Packages into vesicles for secretion or lysosome formation (trans face)

Lysosomes

Membrane-bound vesicles produced by the Golgi. Contain hydrolytic enzymes. Functions:

Digest worn-out organelles (autophagy)

Destroy ingested pathogens in phagocytes

Release enzymes during apoptosis (programmed cell death)

Cell Wall, Vacuole & Cell-Surface Membrane

StructurePresent InCompositionFunction

Cell-surface membraneAll eukaryotic cellsPhospholipid bilayer + embedded proteins (fluid mosaic model)Selectively permeable ; controls entry/exit of substances; cell signalling

Cell wallPlants/algae: cellulose; Fungi: chitin; Prokaryotes: mureinPlants: cellulose microfibrils; Fungi: chitin polymerStructural support; prevents osmotic lysis; fully permeable — does NOT control entry

VacuolePlants (large central vacuole)Bounded by tonoplast ; contains cell sapMaintains turgor pressure; stores pigments, waste products, ions

Most Common Error

The cell wall is fully permeable — it does NOT control what enters the cell. Only the cell-surface membrane is selectively permeable. Confusing these two in exam answers is penalised.

Cell Wall Composition

Plants/algae → Cellulose | Fungi → Chitin | Prokaryotes → Murein (glycoprotein)

The Protein Secretion Pathway

Proteins destined for secretion follow a specific route. Naming it in order is a common 4–6 mark question.

DNA in

Nucleus

mRNA through

Nuclear Pores

Translated on

RER Ribosomes

Protein in

RER Lumen

Transport

Vesicle

Modified in

Golgi

Secretory

Vesicle

Exocytosis

4-Mark Rule

For 4 marks you need 4 named structures/events in the correct order. The most commonly missed step is the transport vesicle from RER to Golgi. Include it explicitly in every answer.

Applied Context

Pancreatic acinar cells secrete digestive enzymes (lipase, amylase). Adaptations: extensive RER for enzyme synthesis; well-developed Golgi for modification and packaging; many secretory vesicles for exocytosis; numerous mitochondria for ATP. A classic exam question — link each organelle to the pathway.

Specialised Cell Adaptations

Apply the same organelle knowledge to unfamiliar specialised cells — the logic is always the same.

CellKey AdaptationsExplanation (HOW it enables function)

SpermMany mitochondria; acrosome (modified lysosome); flagellumMitochondria → ATP for flagellum movement; acrosome → hydrolytic enzymes digest zona pellucida of egg for fertilisation

Root hairLong extension (large SA); many mitochondria; no chloroplastsLarge SA maximises mineral ion absorption; mitochondria → ATP for active transport against concentration gradient; no light underground so no chloroplasts needed

Palisade mesophyllMany chloroplasts near upper surface; thin cell walls; large vacuoleHigh chloroplast density maximises light absorption; thin walls → rapid CO₂ diffusion; vacuole → turgor supports leaf shape

Goblet cellExtensive RER; prominent Golgi; many secretory vesiclesRER → mucin synthesis; Golgi → glycosylation into mucus glycoproteins; vesicles → exocytosis onto epithelial surface

The 3-Part Adaptation Rule

✗ "Root hair cells have many mitochondria." — 1 mark only.

✓ "Root hair cells have many mitochondria, which carry out aerobic respiration, providing ATP for the active transport of mineral ions against their concentration gradient." — 3 marks.

Feature → Process → HOW it enables function.

Centrioles & Organelle Distribution

CENTRIOLES

Paired cylindrical structures made of microtubules. Present in animal cells; absent in most higher plant cells.

Function: Form the spindle fibres during mitosis and meiosis, organising chromosome separation to opposite poles.

Where Are These Structures?

StructureAnimalPlantFungiNucleus✓✓✓Mitochondria✓✓✓Chloroplasts✗✓✗Cell wall✗CelluloseChitinCentral vacuole✗✓✗Centrioles✓✗✗

Exam Tip

The three structures exclusive to plant cells at A level: chloroplasts, large central vacuole, cellulose cell wall. Centrioles are exclusive to animal cells (higher plants do not have them). These are the most frequently tested distinguishing features.

Endosymbiotic Theory

Both mitochondria and chloroplasts evolved from free-living prokaryotes engulfed by a host eukaryotic cell — the endosymbiotic theory.

Evidence

FeatureMitochondria / ChloroplastProkaryoteDNACircular; not associated with histonesCircular; not associated with histonesRibosomes70S (not 80S like cytoplasm)70SReproductionDivide by binary fission independentlyBinary fissionSize~1–5 μm0.5–5 μmMembranesDouble membrane (outer = host; inner = original prokaryote)Single membrane

Synoptic Link — Paper 3

In Paper 3 essays on "evidence in science" or "evolution," two points score highest: (1) circular DNA not associated with histones and (2) 70S ribosomes. Do not just say "they have their own DNA" — specify the type precisely.

Practice Question

A student examines a secretory cell using an electron microscope. They observe: a large nucleus with a prominent nucleolus, extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, numerous secretory vesicles, and many mitochondria.

(a) State the route taken by a secreted protein from synthesis to release. [4 marks]

(b) Explain how the presence of many mitochondria is related to the secretory function. [3 marks]

D:

(a) Protein synthesised on ribosomes of the rough endoplasmic reticulum and enters the RER lumen → transported in transport vesicles to the Golgi apparatus → modified (e.g. glycosylation) and packaged into secretory vesicles → vesicles fuse with cell-surface membrane and protein released by exocytosis.

E:

(b) Mitochondria carry out aerobic respiration, producing ATP. ATP is required for: movement of vesicles along microtubules (motor proteins), active transport of precursor molecules into the cell, and membrane fusion during exocytosis. Without mitochondria, secretory rate would fall significantly.

E:

Named example: Goblet cells in the tracheal epithelium secrete mucus glycoproteins. They show exactly this ultrastructure — extensive RER, prominent Golgi, many secretory vesicles and mitochondria.

P:

In electron micrographs, cells with higher secretory rates have more numerous and larger Golgi cisternae — a quantifiable correlation between Golgi size and secretory output rate.

DEEP Answer: Mitochondrial Adaptations

"Explain how the structure of a mitochondrion is adapted for aerobic respiration." [4 marks]

DEEP CHAIN — MARK-SCORING ANSWER STRUCTURE

D

Define / State the structural featureThe inner mitochondrial membrane is folded inward to form projections called cristae, greatly increasing the surface area of the inner membrane.

E

Explain the mechanismATP synthase is embedded in the inner membrane. The increased surface area provides more attachment sites for ATP synthase, so more ATP is synthesised by oxidative phosphorylation per unit time. The matrix contains Krebs cycle enzymes, enabling complete oxidation of pyruvate.

E

Evidence / Additional featureThe matrix contains circular DNA (not associated with histones) and 70S ribosomes, enabling the mitochondrion to synthesise some of its own proteins — evidence supporting the endosymbiotic theory.

P

Practical / Quantitative linkCells with the highest energy demand (cardiac muscle, sperm) have the greatest cristae density. This is a quantitative relationship: higher cristae density → greater ATP synthase surface area → greater ATP output rate.

Examiner Alerts & Mark-Scoring Vocabulary

Summary

Core Organelles — Structure & Function

OrganelleKey Structural FeatureKey Function

NucleusDouble envelope; nuclear pores; nucleolus; chromatin (DNA + histones)Contains DNA; controls gene expression; rRNA production

MitochondrionCristae; matrix; circular DNA; 70S ribosomesAerobic respiration; ATP production

ChloroplastGrana (thylakoids); stroma; circular DNA; 70S ribosomesPhotosynthesis — light-dep. on thylakoids; Calvin in stroma

RERCisternae with ribosomesProtein synthesis and transport toward Golgi

Golgi apparatusStacked cisternae; cis/trans faces; vesiclesModify (glycosylation) and package proteins; produce lysosomes

SERCisternae; no ribosomesLipid/steroid synthesis; detoxification

LysosomeMembrane-bound vesicle + hydrolytic enzymesReleases hydrolytic enzymes; intracellular digestion; apoptosis

Ribosome2 subunits of rRNA + protein; 80S (euk. cytoplasm); 70S (prokaryotes, mito, chloroplasts)Protein synthesis (translation)

CentriolesPaired cylinders of microtubules; animal cells onlyForm spindle fibres during mitosis/meiosis

Vacuole (plants)Large, central; bounded by tonoplastTurgor pressure; storage of pigments, ions, waste

Cell wall (plants)Cellulose microfibrils; fully permeableStructural support; prevents osmotic lysis

Secretion Pathway

Ribosome (RER) → RER lumen → Transport vesicle → Golgi (modification) → Secretory vesicle → Exocytosis

Endosymbiosis — Two Key Points

Mitochondria and chloroplasts: (1) circular DNA not associated with histones; (2) 70S ribosomes. Both match prokaryotic features — not eukaryotic.

Exam Tip

Every adaptation question follows the same logic: structural feature → maximises function. The words surface area, concentration gradient, and ATP appear in the majority of high-scoring cell answers. Learn to deploy them with precision.