Cell: The Unit of Life

The chapter builds outward from a single idea — the cell theory — to the full architecture of a working cell. It opens with what a cell is and why the theory took three scientists (Schleiden, Schwann, Virchow) to complete. It then gives a bird's-eye overview of cell size, shape and the prokaryotic-eukaryotic divide, before descending into the prokaryotic cell's own compact anatomy: its layered envelope, its mesosomes, flagella, pili and inclusion bodies. The second half is a tour of the eukaryotic cell, organelle by organelle — the plasma membrane and how molecules cross it, the plant cell wall, the coordinated endomembrane system (ER, Golgi apparatus, lysosomes, vacuoles), the semi-autonomous mitochondria and plastids, ribosomes, the cytoskeleton, cilia and flagella, the centrosome, and finally the nucleus and the classification of chromosomes by centromere position.

The cell theory: why the cell is life's basic unit

A unicellular organism — an amoeba, a bacterium, a single yeast cell — can do everything life requires: take in nutrients, respire, excrete, respond, and reproduce, all within one cell. Anything less than a complete cell cannot manage independent living, which is why the cell, not some smaller piece of it, is defined as the fundamental structural and functional unit of all living organisms. Antonie van Leeuwenhoek first saw and described a live cell; Robert Brown later discovered the nucleus; and it was the invention and steady improvement of the microscope, culminating in the electron microscope, that eventually revealed every structural detail described in this chapter. The theory that formalised this was built in stages. In 1838 the German botanist Matthias Schleiden, having examined a large number of plants, reported that all plants are made of different kinds of cells that together form the plant's tissues. In 1839 the German zoologist Theodor Schwann, studying animal cells, found that they too share a thin outer layer — what we now call the plasma membrane — and, from his work on plants, concluded that a cell wall is a feature unique to plant cells. On this basis Schwann proposed that the bodies of both animals and plants are built of cells and the products of cells; together with Schleiden, this became the cell theory. One gap remained: neither Schleiden nor Schwann explained where new cells came from. Rudolf Virchow closed it in 1855 with the principle Omnis cellula-e cellula — cells divide, and new cells arise only from pre-existing cells. The cell theory as accepted today therefore states two things: all living organisms are composed of cells and products of cells, and all cells arise from pre-existing cells.

Prokaryotic versus eukaryotic organisation, and the range of cell size

Every cell, whatever else it does or doesn't have, is built around the same three elements: a delimiting membrane, a semi-fluid matrix called the cytoplasm that is the main arena of cellular chemistry, and genetic material. The line that splits the living world runs through where that genetic material sits. In eukaryotic cells the DNA, organised as chromosomes, is enclosed within a dense, membrane-bound nucleus; eukaryotic cells also possess distinct membrane-bound organelles inside the cytoplasm — endoplasmic reticulum, Golgi complex, lysosomes, mitochondria, microbodies and vacuoles. In prokaryotic cells there is no membrane-bound nucleus at all — the genetic material is naked, not wrapped in a nuclear envelope — and prokaryotic cells lack membrane-bound organelles altogether, with one universal exception: ribosomes, which are non-membrane-bound and are found in every cell, prokaryotic and eukaryotic alike, including inside chloroplasts and mitochondria and studded on rough ER. Animal cells additionally possess a non-membrane-bound organelle called the centrosome, involved in cell division. Cells span an enormous range of size, shape and activity. Mycoplasmas, the smallest cells known, are only about 0.3 micrometre in length; typical bacteria run 3 to 5 micrometres. The largest single isolated cell known is the egg of an ostrich. Among multicellular organisms a human red blood cell is about 7.0 micrometres across, while nerve cells, thanks to their long axons, are some of the longest cells in the body. Shape varies just as widely — disc-like red blood cells, amoeboid white blood cells, long branched nerve cells, elongated tracheids, columnar epithelial cells, round mesophyll cells — and shape is very often tuned to the function a cell performs.

Inside a prokaryotic cell — envelope, motility, and inclusions

Prokaryotes — bacteria, blue-green algae (cyanobacteria), mycoplasma and PPLO (Pleuro Pneumonia Like Organisms) — are generally smaller and multiply far faster than eukaryotic cells, and although they range widely in shape, their internal organisation is fundamentally similar throughout the group. Bacteria come in four basic shapes: bacillus (rod-like), coccus (spherical), vibrio (comma-shaped) and spirillum (spiral). There is no well-defined nucleus; the genomic DNA forms a single circular chromosome lying free in the cytoplasm, and many bacteria additionally carry small circular DNA molecules outside the genomic DNA called plasmids, which confer specific phenotypic traits such as antibiotic resistance and are, in later biotechnology, exploited to carry foreign DNA into bacteria. Most prokaryotic cells, particularly bacteria, wrap themselves in a chemically complex cell envelope of three tightly bound layers acting as a single protective unit: the outermost glycocalyx, then the cell wall, then the plasma membrane (present in all prokaryotes except mycoplasma, which has no wall at all). The glycocalyx varies from a loose slime layer to a thick, tough capsule. The cell wall gives the cell its shape and structural strength, stopping it from bursting or collapsing, and it is differences in this envelope — read out by their response to Gram's staining procedure — that split bacteria into Gram-positive and Gram-negative groups. The plasma membrane beneath is selectively permeable and structurally similar to that of eukaryotes. A distinctive prokaryotic structure is the mesosome, an infolding of the plasma membrane extending into the cell as vesicles, tubules or lamellae; mesosomes assist cell wall formation, DNA replication and its distribution to daughter cells, and also help with respiration, secretion and effectively increasing the membrane's surface area and enzyme content. Some prokaryotes, such as cyanobacteria, have further membranous extensions called chromatophores that carry pigments. Motile bacteria bear thin filamentous flagella, built of three parts — filament, hook and basal body — with the filament, the longest section, projecting outward from the cell surface. Non-motility-related surface structures include pili, elongated tubular structures of a special protein, and fimbriae, small bristle-like fibres that in some bacteria help attach the cell to rocks in streams or to host tissue. Prokaryotic ribosomes, about 15 by 20 nanometres, are associated with the plasma membrane; they are 70S, built of a 50S and a 30S subunit, and several strung along one mRNA form a chain called a polyribosome or polysome. Reserve material is stored in the cytoplasm as inclusion bodies — phosphate granules, cyanophycean granules and glycogen granules — none bound by any membrane; gas vacuoles occur in blue-green and in purple and green photosynthetic bacteria.

The plasma membrane — fluid mosaic model and traffic across it

The detailed structure of the cell membrane became clear only after the electron microscope arrived in the 1950s, though chemical studies on human red blood cells (RBCs) had already told scientists what it was mostly made of: lipids and proteins. The major lipids are phospholipids arranged as a bilayer, with the polar heads facing outward into the watery surroundings on both sides and the hydrophobic tails tucked into the interior, away from water; the membrane also contains cholesterol. The ratio of protein to lipid varies with cell type — in the human erythrocyte membrane it is about 52 per cent protein and 40 per cent lipid, with the remainder made up of carbohydrate. Membrane proteins are classed, by how easily they can be extracted, as peripheral (lying on the surface) or integral (partly or wholly buried within the bilayer). Singer and Nicolson's 1972 fluid mosaic model remains the accepted picture: the lipid bilayer is quasi-fluid, which lets proteins drift laterally within it — a movement measured as the membrane's fluidity — so the whole assembly resembles a mosaic of protein "tiles" floating in a fluid lipid "sea." This fluidity matters for cell growth, the formation of junctions between cells, secretion, endocytosis and cell division. One of the membrane's most important jobs is selectively controlling what crosses it. Small neutral solutes may move across by simple diffusion, travelling from higher to lower concentration with no energy cost; water crossing by diffusion is specifically called osmosis. Polar molecules cannot slip through the nonpolar lipid interior directly, so they need a carrier protein of the membrane to ferry them across — still without spending energy, if moving down the gradient. Some ions or molecules, however, must be moved from a region of lower to a region of higher concentration, against their gradient; this is an energy-dependent process called active transport, which consumes ATP, the textbook example being the Na+/K+ pump.

The cell wall of plants and fungi

A non-living, rigid cell wall forms the outer covering of fungal and plant cells, lying just outside the plasma membrane. Beyond giving the cell its shape, the wall protects against mechanical damage and infection, assists cell-to-cell interaction, and provides a barrier against undesirable macromolecules. In algae the wall is built of cellulose, galactans, mannans and minerals such as calcium carbonate; in other plants it is cellulose, hemicellulose, pectins and protein. A young plant cell's primary wall is capable of further growth; as the cell matures this capacity diminishes and a secondary wall is laid down on the inner, membrane-facing side. The middle lamella, chiefly calcium pectate, glues neighbouring cells together, and both the cell wall and the middle lamella may be crossed by plasmodesmata, channels that connect the cytoplasm of adjoining cells.

The endomembrane system — ER, Golgi apparatus, lysosomes and vacuoles

Several membranous organelles, though structurally and functionally distinct on their own, are grouped together as the endomembrane system because their activities are coordinated: the endoplasmic reticulum, the Golgi complex, lysosomes and vacuoles. Mitochondria, chloroplasts and peroxisomes are deliberately excluded from this grouping — not because they lack membranes, but because their functions are not coordinated with the rest of the set. The endoplasmic reticulum (ER) is a reticulum of tiny tubular structures scattered through the cytoplasm, dividing intracellular space into a luminal (inside the ER) and an extra-luminal (cytoplasmic) compartment. Where ribosomes stud its outer surface it is called rough ER (RER), common in cells actively engaged in protein synthesis and secretion, and continuous with the outer nuclear membrane; where ribosomes are absent it looks smooth and is called smooth ER (SER), the chief site of lipid synthesis, including, in animal cells, steroidal hormones. The Golgi apparatus, first observed by Camillo Golgi in 1898 as densely stained reticular structures near the nucleus, is a stack of flat, disc-shaped sacs called cisternae, 0.5 to 1.0 micrometre across, arranged concentrically near the nucleus with a convex cis (forming) face and a concave trans (maturing) face — distinct but interconnected. Vesicles budding from the ER fuse with the cis face, move through the stack toward the trans face, and are released there, which is why the Golgi apparatus stays closely associated with the ER. Along the way, proteins made on ER-bound ribosomes are modified within the cisternae; the Golgi apparatus is the principal site where glycoproteins and glycolipids are formed.

Lysosomes are membrane-bound vesicles produced by Golgi packaging, and are rich in hydrolytic enzymes — lipases, proteases, carbohydrases, collectively hydrolases — that work optimally at acidic pH and can digest carbohydrates, proteins, lipids and nucleic acids. Vacuoles are membrane-bound spaces in the cytoplasm, bound by a single membrane called the tonoplast, containing water, cell sap, excretory products and other unwanted materials; in plant cells the vacuole can occupy up to 90 per cent of cell volume, and the tonoplast actively transports ions and other materials against their concentration gradient into it, so their concentration there runs far higher than in the cytoplasm. In Amoeba, a specialised contractile vacuole manages osmoregulation and excretion; in many protists, food vacuoles form by engulfing food particles.

Mitochondria and plastids — the semi-autonomous organelles

Mitochondria are typically sausage-shaped or cylindrical, 0.2 to 1.0 micrometre in diameter (average 0.5 micrometre) and 1.0 to 4.1 micrometres long, though their number per cell varies with how metabolically active the cell is. Each is bound by two membranes that divide its interior into an outer and an inner compartment. The outer membrane forms a smooth, continuous boundary; the inner membrane folds inward repeatedly to form cristae, which increase the surface area available for the enzymes of respiration, and the two membranes carry their own distinct sets of these enzymes. The inner compartment is filled with a dense homogeneous matrix, which also holds a single circular DNA molecule, a few RNA molecules, and 70S ribosomes — the full machinery needed to synthesise some of its own proteins. Mitochondria are the site of aerobic respiration and generate the cell's ATP, which is why they are called the "power houses" of the cell; they divide by fission, independently of the cell cycle.

Plastids occur in all plant cells and in euglenoids, and are classified by pigment into chloroplasts, chromoplasts and leucoplasts. Chloroplasts carry chlorophyll and carotenoid pigments that trap light energy for photosynthesis; most occur in the mesophyll cells of leaves, are lens-shaped, oval, spherical, discoid or ribbon-like, 5 to 10 micrometres long and 2 to 4 micrometres wide, numbering as few as one per cell in the green alga Chlamydomonas or 20 to 40 per mesophyll cell. Like mitochondria, chloroplasts are double membrane-bound, with the inner membrane relatively less permeable; the space it encloses is the stroma, which holds stacks of flattened membranous sacs called thylakoids. Thylakoids pile up like a stack of coins into grana (singular granum), and flat tubules called stroma lamellae connect thylakoids of different grana; the thylakoid membrane encloses a space called the lumen, and chlorophyll sits in the thylakoid membranes. The stroma itself carries the enzymes needed for carbohydrate and protein synthesis, plus small circular double-stranded DNA and its own ribosomes — 70S, smaller than the 80S ribosomes floating in the surrounding cytoplasm. Chromoplasts carry fat-soluble carotenoid pigments such as carotene and xanthophylls, giving parts of the plant their yellow, orange or red colour. Leucoplasts are colourless plastids of varied shape that store nutrients: amyloplasts store carbohydrate as starch (as in potato), elaioplasts store oils and fats, and aleuroplasts store protein.

Ribosomes, the cytoskeleton, and cilia and flagella

Ribosomes were first seen as dense granular particles under the electron microscope by George Palade in 1953. Built of RNA and protein and bound by no membrane, they occur in every kind of cell. Eukaryotic ribosomes are 80S, made of a 60S and a 40S subunit; prokaryotic ribosomes are 70S, made of a 50S and a 30S subunit. The "S" stands for the Svedberg unit, the sedimentation coefficient — an indirect measure of a particle's density and size, not a simple length, which is why the subunit values do not add up arithmetically to the whole. The cytoskeleton is an elaborate cytoplasmic network of filamentous proteins — microtubules, microfilaments and intermediate filaments — supplying mechanical support, enabling motility, and maintaining the cell's shape. Cilia and flagella are hair-like outgrowths of the cell membrane: cilia are short and work like oars to move the cell or the fluid around it; flagella are longer and drive cell movement (prokaryotic flagella, described earlier, are structurally different from the eukaryotic kind). Both are covered by the plasma membrane and built around a core called the axoneme, a bundle of microtubules running parallel to the long axis in a characteristic 9+2 array — nine peripheral doublets of microtubules arranged radially around a central pair. The central pair is joined by bridges and wrapped in a central sheath, which links to each peripheral doublet by a radial spoke — nine spokes in all — while the peripheral doublets are themselves interconnected by linkers. Both cilium and flagellum arise from a centriole-like structure at their base called the basal body.

Centrosome and centrioles

The centrosome is an organelle usually containing two cylindrical centrioles, surrounded by amorphous pericentriolar material, with the two centrioles lying perpendicular to each other, each organised like a cartwheel. Each centriole is built of nine evenly spaced peripheral fibrils of the protein tubulin, every fibril a triplet, with adjacent triplets linked together; the proteinaceous centre of the centriole's proximal region, the hub, connects to the peripheral triplets by protein radial spokes. Centrioles form the basal body of cilia and flagella, and in animal cells they also give rise to the spindle fibres of the spindle apparatus during cell division.

The nucleus — envelope, chromatin, and chromosome architecture

The nucleus was first described by Robert Brown in 1831; its stainable material was later named chromatin by Flemming. In the interphase nucleus — the nucleus of a cell that is not dividing — the DNA exists as highly extended, elaborate nucleoprotein fibres of chromatin, set in a nuclear matrix (nucleoplasm) alongside one or more spherical nucleoli. Electron microscopy shows the nuclear envelope as two parallel membranes separated by a perinuclear space of 10 to 50 nanometres, forming the barrier between the nucleus's contents and the cytoplasm. The outer membrane usually stays continuous with the ER and bears ribosomes of its own. At many points this envelope is interrupted by nuclear pores, formed where the two membranes fuse, and these pores are the passages through which RNA and protein move in both directions between nucleus and cytoplasm. Most cells have one nucleus, though multinucleate variations occur, and some mature cells lose their nucleus altogether — mammalian erythrocytes and the sieve tube cells of vascular plants are the standard examples. The nucleolus, not itself membrane-bound and continuous with the surrounding nucleoplasm, is the site of active ribosomal RNA synthesis; cells busy with protein synthesis tend to have larger and more numerous nucleoli. Chromatin is built of DNA together with basic proteins called histones, some non-histone proteins, and RNA. A single human cell packs roughly two metres of DNA thread into just forty-six chromosomes (twenty-three pairs). A chromosome, visible only during cell division, carries a primary constriction, the centromere, flanked by disc-shaped kinetochores; the centromere is what holds the two sister chromatids of a chromosome together. Chromosomes are classified by where the centromere sits: metacentric (centromere in the middle, two equal arms), sub-metacentric (centromere slightly off-centre, one shorter and one longer arm), acrocentric (centromere close to one end, one very short arm and one very long arm), and telocentric (centromere at the very terminus). Some chromosomes additionally carry a non-staining secondary constriction at a fixed location, giving the appearance of a small fragment called a satellite.

Microbodies

Many small, membrane-bound vesicles called microbodies, carrying a variety of enzymes, occur in both plant and animal cells, adding one more layer of enzyme compartmentalisation beyond the endomembrane system proper.

Board level - Distinguishing a plant cell from an animal cell

State three structural features that let you tell, from a labelled diagram alone, whether a cell is a typical plant cell or a typical animal cell.

Step 1. Look for a cell wall outside the plasma membrane. Plant cells have a rigid, non-living cell wall of cellulose, hemicellulose, pectin and protein; animal cells have no cell wall at all, only the plasma membrane as their outer boundary.

Step 2. Look for plastids and a large central vacuole. Plant cells commonly contain plastids (chloroplasts, chromoplasts or leucoplasts) and a large vacuole that can occupy up to 90 per cent of the cell's volume, bound by the tonoplast; animal cells lack plastids entirely, and any vacuoles they have are small and few.

Step 3. Look for centrioles. Animal cells possess centrioles within the centrosome, used to organise the spindle apparatus during division; centrioles are absent in almost all plant cells. Answer: a cell wall, plastids with a large tonoplast-bound vacuole, and absent centrioles mark it as a typical plant cell; no cell wall, no plastids, a small vacuole (if any), and present centrioles mark it as a typical animal cell.

Board level - Reasoning out the functions of a mesosome

What is a mesosome in a prokaryotic cell, and what would you expect to go wrong for a bacterium if its mesosomes failed to form?

Step 1. Identify the structure. A mesosome is an infolding of the bacterial plasma membrane, extending into the cell interior as vesicles, tubules or lamellae — it is not a separate membrane-bound organelle but a specialised extension of the plasma membrane itself.

Step 2. List its known roles from the chapter: mesosomes assist cell wall formation, help in DNA replication and the distribution of replicated DNA to daughter cells, aid respiration and secretion, and effectively increase the plasma membrane's surface area and its enzyme content.

Step 3. Reason out the consequence of losing them. Since mesosomes help partition replicated DNA to daughter cells during division, a bacterium without functional mesosomes would be expected to divide unevenly or unreliably; since they also assist cell wall formation and respiration, wall synthesis after division and the cell's respiratory efficiency would both be impaired, and the reduced membrane surface area would mean fewer sites for membrane-associated enzymes to work. Answer: a mesosome is a membranous infolding of the plasma membrane that supports cell wall formation, DNA replication and partitioning, respiration and secretion, and its loss would be expected to disrupt cell division, wall synthesis and respiratory efficiency together.

Competitive level (NEET) - How much DNA is packed into one chromosome

A single human somatic cell contains approximately 2 metres of DNA distributed among its 46 chromosomes. Estimate the average contour length of DNA packed into one chromosome, in micrometres, and state what this tells you about the degree of DNA packaging inside the nucleus.

Step 1. Convert the total DNA length to a convenient unit. Total DNA length is 2 metres, which is $2 \times 10^{6}\ \mu\text{m}$ (since $1\ \text{m} = 10^{6}\ \mu\text{m}$).

Step 2. Divide by the number of chromosomes. Average DNA per chromosome is $\dfrac{2 \times 10^{6}\ \mu\text{m}}{46} \approx 4.3 \times 10^{4}\ \mu\text{m}$, that is, roughly 43,000 micrometres, or about 4.3 centimetres of DNA thread per chromosome on average.

Step 3. Compare this to the size of the structure it must fit into. A condensed metaphase chromosome is only a few micrometres long, yet it must contain a thread on the order of tens of thousands of micrometres. Answer: about $4.3 \times 10^{4}\ \mu\text{m}$ (roughly 43,000 micrometres, or 4.3 cm) of DNA is packed into the average chromosome, showing that the DNA inside a chromosome must be coiled and folded through an enormous compaction ratio — many thousand-fold — around histone proteins to fit inside a structure only a few micrometres long. Timing note: about ninety seconds. The whole problem is one division and one unit conversion — the only trap is forgetting that $1\ \text{m} = 10^{6}\ \mu\text{m}$, not $10^{3}$, so double-check the power of ten before dividing by 46.

Several confusions recur in this chapter beyond the single biggest one flagged below. Students often assume every cell has a nucleus and a cell wall — mature mammalian erythrocytes and sieve tube cells lack a nucleus, and only plant and fungal cells (not animal cells) have a cell wall. Ribosomes are frequently mis-sorted as membrane-bound organelles simply because they sit on the ER or float in the cytoplasm near other membranes; they are not membrane-bound at all, and they are the one organelle common to both prokaryotic and eukaryotic cells. The Svedberg unit (S) is often treated as if it adds up like a length — 50S plus 30S is quoted as if it should equal 80S, when the correct sum is 70S, because S measures sedimentation behaviour (a function of both size and shape), not simple mass or length. Finally, "prokaryotic cells have no organelles" is stated too broadly — prokaryotes do have ribosomes, and inclusion bodies and mesosomes, but strictly lack the true membrane-bound organelles (ER, Golgi apparatus, mitochondria, and so on) that define eukaryotic cytoplasm.

• State the two propositions of the cell theory and name the three scientists credited with each part.
• Explain, in one sentence, the single structural criterion that distinguishes a prokaryotic cell from a eukaryotic cell.
• List the three layers of a bacterial cell envelope in order, and describe what a mesosome is and does.
• Describe the fluid mosaic model of the plasma membrane and distinguish simple diffusion, osmosis, facilitated diffusion and active transport by whether they need a carrier and whether they need energy.
• Name every organelle that belongs to the endomembrane system and explain, with a reason, why mitochondria, chloroplasts and peroxisomes are excluded from it.
• Compare the structure of a mitochondrion and a chloroplast, and explain what "semi-autonomous" means for both.
• Distinguish 70S from 80S ribosomes by their subunits and by which kinds of cells and organelles contain each.
• Describe the 9+2 arrangement of the axoneme in cilia and flagella, and the structure of a centriole.
• Classify a chromosome as metacentric, sub-metacentric, acrocentric or telocentric from a diagram showing its centromere position.
• Describe the structure of the nuclear envelope, explain the role of nuclear pores, and state two examples of mature cells that lack a nucleus.

Ask the tutor: Want to work through labelling a full plant-cell or animal-cell diagram from scratch, or practise classifying chromosomes from arm-length diagrams for your next test?