Cells as the basic units of living organisms

The nucleus is the largest organelle of a typical eukaryotic cell, usually 5–10 μm across. It is bounded by a double-membrane nuclear envelope continuous with the rough endoplasmic reticulum, and perforated by approximately 3000 nuclear pores per nucleus. Each pore is a protein complex that controls regulated transport — mRNA and ribosomal subunits move OUT, transcription factors and DNA-repair enzymes move IN.

Inside the envelope, the nucleoplasm contains chromatin — long molecules of DNA wound around histone proteins. Tightly-packed inactive regions are called heterochromatin (electron-dense in micrographs); loosely-packed transcriptionally-active regions are called euchromatin. During mitosis the chromatin condenses further into visible chromosomes.

One or more dense, darkly-staining regions called nucleoli are visible inside the nucleus. The nucleolus is the site of synthesis of ribosomal RNA (rRNA) and of assembly of the large and small ribosomal subunits before their export through the nuclear pores.

Function summary. The nucleus controls the cell by regulating which genes are transcribed and therefore which proteins are made. By keeping the DNA inside an envelope, the cell separates transcription (and splicing of pre-mRNA) from cytoplasmic translation.

The endoplasmic reticulum is a network of flattened membrane sacs called cisternae that extends throughout the cytoplasm and is continuous with the outer nuclear membrane.

Rough endoplasmic reticulum (rER). The cytoplasmic surface is studded with 80S ribosomes — this gives the ‘rough’ appearance in electron micrographs. Newly translated polypeptides destined for secretion or for insertion into a membrane are threaded through a channel in the rER membrane and enter the rER lumen, where they fold and may be modified (e.g. disulfide bridge formation). Quality control rejects misfolded proteins. Properly folded products are pinched off in transport vesicles that bud from the rER membrane and move to the Golgi apparatus.

Smooth endoplasmic reticulum (sER). No ribosomes attached. Functions include:

• Lipid synthesis — phospholipids (for new membranes), cholesterol, steroid hormones.
• Detoxification of drugs and metabolites (especially abundant in liver cells).
• Calcium-ion storage and release — particularly important in muscle cells, where the sER (called sarcoplasmic reticulum) releases Ca²⁺ to trigger contraction.

Both rER and sER are continuous with the nuclear envelope, and the ER as a whole is sometimes regarded as the largest membrane system in the cell.

The Golgi apparatus (or Golgi body) is a stack of typically 4–8 flattened membrane-bound sacs called cisternae arranged in a curved stack. Proteins enter the Golgi at the curved cis face (closer to the rER) and leave at the trans face (closer to the cell-surface membrane).

Functions.

• Modification. Proteins are processed as they move through the stack — most importantly by glycosylation (addition of carbohydrate side chains), but also by trimming, phosphorylation and sulfation. The mature products are glycoproteins.
• Sorting. Proteins carrying different destination tags are sorted into different vesicles at the trans face.
• Packaging. Finished proteins are packaged into secretory vesicles for export, into lysosomes (carrying acid hydrolases), or into vesicles destined for the cell-surface membrane.
• Synthesis of polysaccharides. Plant Golgi apparatuses synthesise cell-wall polysaccharides (pectin, hemicellulose) and dispatch them to the cell wall in vesicles.

The Golgi is especially prominent in cells that secrete heavily — pancreatic acinar cells (digestive enzymes), plasma cells (antibodies) and goblet cells (mucus).

Mitochondria are rod-shaped or oval organelles roughly 0.5–2 μm long. Two phospholipid bilayer membranes enclose the organelle:

• The outer membrane is smooth and permeable to small molecules.
• The inner membrane is highly folded into invaginations called cristae, greatly increasing the surface area within a small volume. The cristae carry the protein complexes of the electron transport chain and the ATP synthase enzyme used in oxidative phosphorylation.

The fluid space inside the inner membrane is the matrix. It contains:

• Enzymes of the Krebs (citric-acid) cycle and of the link reaction.
• A loop of circular DNA (the mitochondrial genome).
• 70S ribosomes — smaller than the cell's 80S cytoplasmic ribosomes, similar to those of bacteria.

The presence of 70S ribosomes and circular DNA is the main piece of evidence for the endosymbiotic theory of mitochondrial origin — that mitochondria descend from free-living α-proteobacteria engulfed by an ancestral eukaryote.

Cell-type variation. Cells with high ATP demand contain large numbers of mitochondria — for example, muscle fibres, kidney tubule cells, sperm cells (in the mid-piece) and neurons.

Chloroplasts are large oval organelles, typically 5–10 μm long, found in photosynthetic tissues of plants and algae. They are bounded by a double envelope (outer + inner phospholipid bilayer membrane), with an intermembrane space of negligible function.

Inside the inner membrane, a third internal membrane system forms flattened sacs called thylakoids, which are stacked into structures called grana (singular: granum). Adjacent grana are connected by membrane bridges called intergranal lamellae.

Functional layout.

• Thylakoid membranes carry chlorophyll (in light-harvesting complexes), the photosystems, the electron transport chain and the ATP synthase used in the light-dependent reactions of photosynthesis.
• Stroma is the aqueous matrix surrounding the thylakoids. It contains the enzymes of the Calvin cycle (notably rubisco) for the light-independent reactions, plus:
  • Circular DNA — the chloroplast genome.
  • 70S ribosomes — similar to bacterial ribosomes.
  • Starch grains — short-term carbohydrate store.
  • Lipid droplets — store membrane lipids.

The combination of own DNA and 70S ribosomes provides evidence for an endosymbiotic origin of chloroplasts from free-living cyanobacteria. Chloroplasts are found ONLY in plants and algae — animal and fungal cells contain none.

Lysosomes are small (0.1–1 μm) single-membrane spherical vesicles containing hydrolytic enzymes (proteases, lipases, nucleases, glycosidases) at acidic pH 4.5–5. They digest:

• Engulfed material (phagocytosis) — bacteria in macrophages and neutrophils.
• Worn-out organelles (autophagy) — old mitochondria recycled into amino acids and nucleotides.
• The cell itself, by controlled release of enzymes during apoptosis.

The acid pH is maintained by H⁺-ATPase pumps in the lysosome membrane. The membrane protects the rest of the cell from the enzymes inside.

Vesicles are general-purpose membrane-bound spheres used to shuttle material between organelles (rER → Golgi, Golgi → cell-surface membrane) and between the inside and outside of the cell (endocytosis, exocytosis).

Ribosomes are large ribonucleoprotein particles (NOT membrane-bound) made of rRNA and proteins. They are the site of translation. Eukaryotic cytoplasmic ribosomes are 80S (consisting of a 60S + a 40S subunit). Ribosomes inside mitochondria and chloroplasts — and the ribosomes of all prokaryotes — are smaller 70S ribosomes (50S + 30S). Free ribosomes in the cytoplasm make cytosolic proteins; ribosomes attached to the rER make proteins for export.

Centrioles are short hollow cylinders of microtubules — 9 triplets arranged in a ring with no central pair — found in pairs near the nucleus of animal cells. They organise the microtubule spindle during mitosis. Centrioles are absent from flowering plant cells, where the spindle is organised from microtubule organising centres in the cytoplasm instead.

The cytoskeleton is a three-dimensional network of protein filaments that pervades the cytoplasm of every eukaryotic cell. Three types of filament:

• Microtubules — hollow cylinders of α/β-tubulin, ~25 nm diameter. Form spindle fibres, tracks for vesicle transport (with motor proteins kinesin and dynein), and the core of cilia and flagella.
• Actin microfilaments — solid filaments of polymerised actin, ~7 nm diameter. Generate contractile forces, drive cytoplasmic streaming, form the contractile ring during cytokinesis.
• Intermediate filaments — ropes of various proteins (e.g. keratin), ~10 nm diameter. Provide mechanical strength and anchor organelles.

Cilia and flagella (eukaryotic) share the same internal structure called an axoneme: a ring of 9 pairs of microtubules around a central pair — the ‘9+2’ arrangement — surrounded by an extension of the cell-surface membrane. Motor protein dynein arms slide adjacent microtubule pairs over each other, bending the structure and producing wave-like beating.

• Cilia are short and present in large numbers per cell. They beat in coordinated waves — e.g. the cilia of ciliated epithelial cells in the trachea sweep mucus and trapped dust up away from the lungs.
• Flagella are longer and usually single (e.g. the tail of a sperm cell). They propel the whole cell.

Note. The bacterial flagellum is completely different — it is built from the protein flagellin (not microtubules), has no 9+2 structure, and rotates rather than waving.

Every cell — eukaryotic or prokaryotic — is bounded by a cell-surface membrane (also called the plasma membrane). It is a phospholipid bilayer with embedded proteins (full fluid-mosaic model is the focus of subtopic 4.1). It controls what enters and leaves the cell, carries receptors for cell signalling, and underlies cell recognition.

Beyond the cell-surface membrane, some cells have an additional cell wall:

• Plant cell wall. Cellulose microfibrils embedded in a matrix of hemicellulose and pectin. Provides mechanical strength, prevents bursting in hypotonic conditions, and shapes the cell. Adjacent plant cells are connected through pores in the wall called plasmodesmata, which allow continuity of cytoplasm.
• Fungal cell wall. Chitin — a polymer of N-acetylglucosamine, the same polymer as insect exoskeleton.
• Bacterial cell wall. Peptidoglycan (also called murein) — a polymer of sugars cross-linked by short peptides. The antibiotic penicillin works by inhibiting peptidoglycan cross-linking, weakening the wall.
• Animal cells. NO cell wall — only the cell-surface membrane.

Plant cells also contain a large central vacuole bounded by a membrane called the tonoplast. It is filled with cell sap (water, sugars, ions, sometimes pigments) and provides turgor pressure that supports the cell. Animal cells may contain small temporary vacuoles but never a large permanent central vacuole.

Several organelles cooperate to synthesise and release an extracellular protein such as insulin or a digestive enzyme. The pathway is a favourite 6–8 mark question.

1. Nucleus. The gene is transcribed; mRNA is processed (splicing, capping, polyadenylation) and exported through a nuclear pore.
2. rER ribosome. mRNA binds to an 80S ribosome on the rER. As the polypeptide is translated, a signal sequence threads it through a channel in the rER membrane into the rER lumen.
3. rER lumen. The polypeptide folds, forms disulfide bridges and is quality-checked. A transport vesicle pinches off from the rER membrane.
4. Cis face of Golgi. The vesicle fuses with the cis face. The protein moves through the stack to the trans face, being modified (glycosylation, trimming).
5. Trans face of Golgi. A secretory vesicle buds off carrying the finished glycoprotein.
6. Cytoskeletal transport. Motor proteins (kinesin) carry the vesicle along microtubule tracks to the cell-surface membrane.
7. Exocytosis. The vesicle membrane fuses with the cell-surface membrane and the protein is released to the outside. The vesicle membrane is recycled.

ATP is required for vesicle transport and fusion — so secretory cells have abundant mitochondria.

Cells specialised for secretion:

• Pancreatic acinar cells — digestive enzymes (amylase, trypsinogen).
• β-cells of the islets of Langerhans — insulin.
• Plasma cells — antibodies (IgG, IgM).
• Goblet cells — mucus.

Bacteria (and the less commonly examined archaea) are prokaryotic — they have a fundamentally different cellular organisation from the eukaryotic cells of animals, plants, fungi and protoctists.

Comparison table.

Feature	Prokaryotic cell	Eukaryotic cell
Size	1–5 μm	10–100 μm
Genetic material	Circular DNA, free in cytoplasm (nucleoid region); plasmids	Linear DNA in nucleus, wound around histones
Nuclear envelope	Absent	Present (double membrane + pores)
Membrane-bound organelles	None	rER, sER, Golgi, mitochondria, lysosomes (and chloroplasts in plants)
Ribosomes	70S	80S in cytoplasm (70S in mitochondria / chloroplasts)
Cell wall	Peptidoglycan (bacteria)	Cellulose (plants), chitin (fungi), absent (animals)
Extra features	Plasmids, pili, bacterial flagellum (flagellin, rotational), capsule	Cytoskeleton, centrioles, cilia / flagella (9+2 microtubule axoneme)
Cell division	Binary fission	Mitosis or meiosis

Plasmids are small circular pieces of extra-chromosomal DNA that often carry accessory genes (antibiotic resistance, virulence factors) and can be transferred between bacteria — the basis of horizontal gene transfer and the spread of antibiotic resistance.

Bacterial respiratory enzymes lie on infoldings of the cell-surface membrane rather than on a separate mitochondrial inner membrane.

Why this matters in medicine. Many antibiotics exploit prokaryote-specific structures:

• Penicillin inhibits peptidoglycan cross-linking → bacterial cell wall weakens.
• Streptomycin and tetracycline bind to the 30S subunit of 70S ribosomes → inhibits bacterial translation without affecting the 80S ribosomes of human cells.

Both animal and plant cells are eukaryotic and share most of the same organelles — nucleus, rER, sER, Golgi, mitochondria, lysosomes, ribosomes, cytoskeleton, cell-surface membrane.

Plant cells have, in addition:

• Cell wall of cellulose microfibrils in a matrix of hemicellulose and pectin.
• Chloroplasts in photosynthetic tissues.
• A large central vacuole bounded by the tonoplast, filled with cell sap.
• Plasmodesmata — pores through the cell wall that connect the cytoplasm of adjacent plant cells.
• Carbohydrate stored as starch grains (often inside chloroplasts).

Animal cells have, in addition:

• Centrioles in pairs near the nucleus — organise spindle fibres during mitosis. (Flowering plants lack centrioles; their spindles are organised differently.)
• Sometimes cilia or flagella (e.g. respiratory epithelium, sperm) — these are present in some plant gametes too, but uncommon in flowering plants.
• Carbohydrate stored as glycogen in cytoplasm (especially in liver and muscle).

Shape. Plant cells tend to be more regularly geometric (rectangular or polygonal) because the cell wall constrains their shape. Animal cells take more varied shapes determined by the cytoskeleton and the cells around them.

Viruses are non-cellular structures. They are not made of cells, do not metabolise, and cannot reproduce outside a living host cell. They consist of:

• A nucleic acid core — either DNA or RNA, single- or double-stranded, depending on the virus.
• A capsid — a protein coat made of repeating protein subunits called capsomeres.
• (Some viruses, e.g. HIV, influenza) an outer envelope of phospholipids derived from the host cell-surface membrane, with embedded viral glycoprotein spikes used to bind to host receptors.

Viruses are typically 20–300 nm in diameter — smaller than even the smallest bacteria. They cannot be resolved by a light microscope and require electron microscopy.

Viruses are not classified as living because they lack the cellular machinery — no ribosomes, no metabolism, no growth, no homeostasis. They hijack the host cell's ribosomes, nucleic-acid synthesis machinery and energy supply to make copies of themselves.