Eukaryotic Cell Ultrastructure: Golgi, Ribosomes, Mitochondria and Lysosomes

Spec Mapping — OCR H420 Module 2.1.1 — Cell structure, content statements covering the ultrastructure of the Golgi apparatus, ribosomes (80S and 70S), mitochondria, and lysosomes, relating structure to function (refer to the official OCR H420 specification document for exact wording). This lesson is the second half of the eukaryotic-ultrastructure pair started in the previous lesson and feeds directly into the synoptic protein-secretion lesson later in the course.

Continuing our tour of eukaryotic organelles, this lesson focuses on the Golgi apparatus, ribosomes (both 80S and 70S), mitochondria, and lysosomes. These organelles are central to protein processing, protein synthesis, energy conversion, and intracellular digestion. OCR 2.1.1 requires that you describe the ultrastructure of each and relate it to function.

The historical attribution is dense in this lesson. Camillo Golgi (1898) identified the eponymous apparatus using silver impregnation in nerve cells. George Palade (1955) characterised the ribosome by electron microscopy and combined it with cell fractionation to trace the secretory pathway. Christian de Duve (1955) discovered lysosomes by differential centrifugation. Lynn Margulis (1967) reframed mitochondria as descendants of engulfed alpha-proteobacteria. Each of these names has appeared on OCR papers in recent years; A* candidates are expected to recognise the underlying paradigm shifts.

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SVG cross-section: mitochondrion and Golgi stack

~6 stacked cisternae

Key features visible in the diagram: the double membrane of the mitochondrion with the inner membrane folded into cristae that drastically increase surface area for the electron transport chain, the matrix containing dark dots that are 70S ribosomes, and the polarised cis → trans architecture of the Golgi stack with vesicles arriving from the RER on the left and departing as secretory vesicles or lysosomes on the right.

Ribosomes

Ribosomes are the sites of translation (protein synthesis), where mRNA is decoded to assemble amino acids into polypeptides. They are not membrane-bound; they are considered organelles in the broad sense because they have a specific structural organisation and function.

Structure of Ribosomes

Ribosomes are ribonucleoproteins (RNP) composed of ribosomal RNA (rRNA) and ribosomal proteins. They exist in two sizes:

Type	Large subunit	Small subunit	Total	Location
80S ribosome	60S	40S	80S	Eukaryotic cytoplasm (free or on RER)
70S ribosome	50S	30S	70S	Prokaryotes, mitochondria, chloroplasts

Key Point: "S" (Svedberg unit) refers to the sedimentation rate in an ultracentrifuge, not a simple measure of mass. This is why 60S + 40S = 80S, rather than 100S — the units are not additive.

Where Are Ribosomes Found?

• Free in the cytoplasm — make proteins that remain inside the cytosol, such as many enzymes.
• Attached to the rough endoplasmic reticulum — make proteins that will be secreted, inserted into the membrane, or sent to lysosomes.
• Inside mitochondria (70S) — make proteins encoded by the mitochondrial genome, essential for oxidative phosphorylation complexes.
• Inside chloroplasts (70S, in plant cells) — make proteins encoded by the chloroplast genome.

Functional Sites on Ribosomes

Each ribosome has three tRNA binding sites:

• A site (aminoacyl) — accepts incoming charged tRNA.
• P site (peptidyl) — holds the tRNA carrying the growing polypeptide.
• E site (exit) — from which the empty tRNA leaves.

The large subunit contains the peptidyl transferase activity, which catalyses peptide bond formation. This activity is itself performed by rRNA (the ribosome is therefore a ribozyme).

Exam Tip: The existence of 70S ribosomes in mitochondria and chloroplasts is powerful evidence for the endosymbiotic theory, which proposes that these organelles evolved from free-living prokaryotes engulfed by an ancestral eukaryotic cell.

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The Golgi Apparatus

The Golgi apparatus (also called the Golgi body or Golgi complex) consists of a stack of 4–8 flattened, membrane-bound cisternae resembling a stack of plates. It is usually located near the nucleus and the RER.

Structural Regions

• Cis face — the receiving side, closest to the RER. Transport vesicles from the RER fuse here.
• Medial cisternae — the middle region where most enzymatic modifications occur.
• Trans face — the dispatching side, furthest from the RER. Vesicles bud off from here to deliver their cargo.

Functions of the Golgi

The Golgi apparatus is the cell's sorting, modifying, and packaging centre. Its main functions are:

1. Modifies proteins and lipids as they pass through the cisternae. Modifications include:
   • Glycosylation — trimming and adding sugars to form mature glycoproteins and glycolipids.
   • Phosphorylation — tagging lysosomal enzymes with mannose-6-phosphate so they are sorted to lysosomes.
   • Proteolytic cleavage — cutting larger precursor proteins into their active forms (e.g., proinsulin → insulin).
2. Sorts molecules according to their final destination (secretion, plasma membrane, lysosome).
3. Packages finished molecules into vesicles that bud from the trans face.
4. Synthesises certain polysaccharides, including plant cell wall components (e.g., pectin and hemicellulose).
5. Forms lysosomes — specialised vesicles containing hydrolytic enzymes.

Vesicles from the Golgi

Three main types of vesicles leave the trans-Golgi network:

• Secretory vesicles — fuse with the plasma membrane to release contents outside the cell (exocytosis).
• Membrane vesicles — incorporate new proteins and lipids into the plasma membrane.
• Lysosomes — remain inside the cell for intracellular digestion.

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Mitochondria

Mitochondria are often described as the powerhouses of the cell because they generate most of the cell's ATP through aerobic respiration. They are typically 1–10 µm long and 0.5–1 µm wide, visible with light microscopy as rods, but their ultrastructure is only revealed by TEM.

Structure

• Double membrane. The outer membrane is smooth and contains porin channels (permeable to small molecules). The inner membrane is highly folded into cristae, which drastically increase surface area for the electron transport chain.
• Matrix — the fluid-filled interior enclosed by the inner membrane. Contains:
  • Enzymes of the Krebs cycle (also called the citric acid cycle or TCA cycle).
  • Mitochondrial DNA — a small circular molecule, maternally inherited.
  • 70S ribosomes — synthesise proteins encoded by mitochondrial DNA.
  • Inorganic ions and substrates.
• Intermembrane space — the region between the outer and inner membranes. The electron transport chain pumps protons (H⁺) into this space, creating a gradient used for ATP synthesis.

Function: Aerobic Respiration

Mitochondria carry out the latter stages of aerobic respiration:

• Link reaction (in the matrix) — pyruvate is converted to acetyl CoA, releasing CO₂ and reduced NAD.
• Krebs cycle (in the matrix) — acetyl CoA is fully oxidised, generating reduced NAD, reduced FAD, ATP, and CO₂.
• Oxidative phosphorylation (on the inner membrane / cristae) — reduced coenzymes donate electrons to the electron transport chain. As electrons pass along protein complexes, H⁺ are pumped into the intermembrane space. The resulting electrochemical gradient drives ATP synthase, which phosphorylates ADP to ATP. Oxygen is the terminal electron acceptor, combining with electrons and H⁺ to form water.

Structural Adaptations Relating to Function

• Many cristae → large surface area for the electron transport chain and ATP synthase.
• Matrix enzymes → Krebs cycle reactions proceed efficiently in a concentrated enzyme environment.
• Double membrane → separates the H⁺ gradient that drives ATP synthesis.
• Own DNA and ribosomes → allow rapid in-house production of some respiratory proteins.

Exam Tip: A cell with large numbers of mitochondria is metabolically very active. Examples: muscle cells (especially cardiac and slow-twitch), active neurons, liver cells, sperm midpiece, epithelial cells with active transport functions.

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Lysosomes

Lysosomes are spherical, single-membrane vesicles, typically 0.1–1 µm in diameter, containing around 40 different hydrolytic enzymes (collectively called lysozymes or acid hydrolases).

Structure

• Single phospholipid bilayer membrane that is chemically resistant to the acidic, enzymatic interior.
• The interior pH is kept around 4.5–5.0 by an ATP-driven proton pump.
• Contains hydrolases active at this low pH: proteases, lipases, nucleases, glycosidases, phosphatases. Keeping the enzymes active only at low pH is a safety mechanism — if a lysosome ruptures and releases its contents into the neutral cytosol, the enzymes are far less active.

Functions of Lysosomes

1. Intracellular digestion of material taken in by endocytosis or phagocytosis. A lysosome fuses with a phagosome to form a phagolysosome, where engulfed bacteria or debris are broken down. This is critical in phagocytic white blood cells (neutrophils, macrophages).
2. Autophagy — digestion of worn-out or damaged organelles. The organelle is first wrapped in a double membrane (an autophagosome), which then fuses with a lysosome.
3. Autolysis — self-destruction of a cell. When a cell dies (e.g., during development or injury), lysosomes release their enzymes and digest cellular contents.
4. Release of enzymes outside the cell (exocytosis) — in specialised situations, such as the acrosome reaction of sperm, where digestive enzymes help penetrate the egg.

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Mitochondrial ATP yield — quantitative depth

A single molecule of glucose, fully oxidised through glycolysis, the link reaction, the Krebs cycle and oxidative phosphorylation, yields approximately 30–32 ATP in eukaryotes. The largest contribution by far is oxidative phosphorylation across the mitochondrial inner membrane. The proton-motive force (a combination of a pH gradient and an electrical gradient across the inner membrane) drives ATP synthase, which rotates as protons pass through it and catalyses the phosphorylation of ADP to ATP. The chemiosmotic theory of Peter Mitchell (1961, Nobel Prize 1978) underpins this — a paradigm shift in bioenergetics paraphrased here as the idea that energy is stored in a transmembrane proton gradient rather than in a high-energy chemical intermediate.

Why cristae?

If the inner mitochondrial membrane were flat rather than folded into cristae, surface area would be limited to the boundary of the outer membrane envelope (~10⁻⁸ m² for a typical mitochondrion). Folding into cristae multiplies this by 5–10× in liver hepatocytes and up to ~20× in cardiac muscle mitochondria. This is the structural reason cardiac muscle cells can pack so many electron-transport chains and ATP synthases per unit cell volume — a key adaptation for the heart's relentless metabolic demand.

Mark-scheme literacy: when explaining mitochondrial structure-function, examiners reward explicit linkage of the cristae → surface area → ETC density → ATP yield chain. A quantitative anchor (5–20× multiplication of surface area) lifts the answer to top-band.

Compartmentalisation as a unifying theme