Eukaryotic cell structure and organelles

What the electron microscope added

A light microscope resolves structures about 0.2 µm apart, so it can show the nucleus, cytoplasm, cell boundary and larger plant-cell structures. Electron microscopy has much greater resolution and reveals cell ultrastructure, including mitochondria, endoplasmic reticulum, Golgi apparatus and ribosomes.

Describe the drawing

An animal cell drawn in section. A large round nucleus with a dense nucleolus inside it sits towards the top, wrapped in a double nuclear envelope. Flattened sacs of rough endoplasmic reticulum studded with ribosomes run beside it, with smooth endoplasmic reticulum free of ribosomes on the other side. A stack of Golgi sacs with vesicles budding off lies below, together with two mitochondria showing folded inner membranes, a lysosome, free ribosomes scattered through the cytoplasm, a pair of centrioles, and the cell-surface membrane enclosing everything. There is no cell wall, chloroplast or vacuole.

Membrane number is a useful structural distinction. The nucleus, mitochondria and chloroplasts have double membranes; the Golgi apparatus, lysosomes, vesicles and endoplasmic reticulum are bounded by a single membrane; ribosomes have no surrounding membrane. In an exam answer, link each structural feature to its function, for example: "Cristae increase the inner-membrane surface available for the electron transport chain and ATP synthase."

Organelle

A structure inside a cell with a distinct function, usually but not always surrounded by its own membrane.

Ultrastructure

The detail of a cell's internal structure as revealed by an electron microscope.

Cytoplasm

Everything inside the cell-surface membrane except the nucleus: the cytosol and the organelles suspended in it.

The nucleus, and two kinds of endoplasmic reticulum

The nucleus is wrapped in two membranes, and the pair together is the nuclear envelope. It is punched through with nuclear pores, a few thousand of them in a typical cell, each around 40 to 100 nm across. Those pores are the reason the arrangement works: they are gateways with transport machinery rather than plain holes, exporting processed messenger RNA selectively while the chromosomes stay inside the envelope, so transcription occurs in the nucleus and translation in the cytoplasm.

Inside, the DNA is wound round histone proteins into chromatin. One patch is denser than the rest and takes up stain more heavily: the nucleolus, where ribosomal RNA is made and the two ribosomal subunits are assembled. A cell with a large nucleolus is building a lot of ribosomes, which usually means it is about to make a lot of protein.

The outer membrane of the nuclear envelope does not stop at the nucleus. It runs straight on into the endoplasmic reticulum, a system of flattened sacs called cisternae folded through the cytoplasm. There are two versions, and the defining structural difference between them is what is stuck to the outside.

Rough endoplasmic reticulum is studded with ribosomes. A protein made on one of those ribosomes is threaded into the sac as the chain grows, so it enters the membrane system at the point of synthesis rather than crossing a membrane later. Proteins for secretion, for lysosomes and for the cell-surface membrane are all made here. A plasma cell pouring out antibody is almost solid rough ER.

Smooth endoplasmic reticulum has no ribosomes on it and a completely different job list: it synthesises lipids, phospholipids and steroids. Liver cells use theirs to break down drugs and alcohol, which is why a liver cell has an unusual amount. In a muscle fibre a specialised version stores calcium ions and releases them to trigger contraction. Abundant smooth endoplasmic reticulum therefore indicates lipid synthesis or, in the liver, drug metabolism.

Nuclear envelope

The double membrane surrounding the nucleus, continuous with the endoplasmic reticulum and perforated by nuclear pores.

Nucleolus

A dense region within the nucleus where ribosomal RNA is made and ribosomes are assembled.

Rough endoplasmic reticulum

Flattened membrane sacs with ribosomes attached, which make and transport proteins for export or for membranes.

Smooth endoplasmic reticulum

Membrane sacs without ribosomes, which synthesise lipids and steroids and store calcium ions.

The secretory pathway

Proteins for secretion, lysosomes or cell-surface membranes are synthesised by ribosomes on the rough endoplasmic reticulum. Transport vesicles carry them to the Golgi apparatus, where they are modified and sorted. Secretory vesicles then carry selected proteins to the cell-surface membrane for exocytosis.

Describe the drawing

A numbered vertical route with six stations joined by downward arrows. Station one is the nucleus, where messenger RNA is made and leaves through a pore. Station two is a ribosome on the rough endoplasmic reticulum, where the protein is assembled. Station three is a transport vesicle budding off the rough endoplasmic reticulum. Station four is the Golgi apparatus, drawn as a stack of sacs, where the protein is modified. Station five is a secretory vesicle. Station six is the cell-surface membrane, drawn as two lines, where the vesicle fuses and the protein is released by exocytosis.

The Golgi apparatus is a stack of flattened sacs, usually four to eight of them, curved and with vesicles budding off one face. Vesicles arrive at one side carrying newly made protein, the contents move through the stack, and finished product leaves the other side. What happens in between is modification: sugars are trimmed and extended to finish glycoproteins (the first sugars are attached back in the ER), chains are cut to length, phosphate groups are attached, and each product is sorted and addressed to its destination. The stack allows a sequence of steps to happen in order, which a single compartment could not do.

Most folding begins in the rough endoplasmic reticulum. The Golgi modifies and sorts proteins; it is not the main site of protein folding. A secreted polypeptide folds as it is made, with chaperone proteins holding it while it does, and reaches the Golgi essentially in shape.

Lysosomes bud from the Golgi as well. The enzymes inside them are proteins, made on rough ER, packaged like any other export and then retained rather than secreted.

The two organelles that handle energy

Mitochondria are usually between 1 and 10 µm long, about the size of a whole bacterium, which is not a coincidence. Each has two membranes. The outer one is smooth. The inner one is folded into cristae. The electron transport chain and ATP synthase are located in that inner membrane, so greater folding gives a larger surface area for them and a higher rate of ATP synthesis. The fluid inside is the matrix, where the Krebs cycle runs, and it contains enzymes, a small loop of DNA and 70S ribosomes of its own.

The number of mitochondria in a cell reflects how much ATP that cell needs. Muscle fibres, sperm cells and the epithelial cells lining the small intestine are all crowded with them; a mature red blood cell has none at all, and no nucleus either.

Chloroplasts, which plant cells have as well as mitochondria, are built on the same plan: a double envelope, a fluid interior called the stroma, and an internal membrane system. Here the membranes form flattened discs called thylakoids, stacked into piles called grana, and the chlorophyll sits in the thylakoid membranes. Stacking gives a large area of pigment-bearing membrane in a small volume, so a lot of light gets absorbed. The stroma holds the enzymes of the light-independent reactions, along with starch grains, a loop of DNA and, again, 70S ribosomes.

Those loops of DNA and small ribosomes are the evidence behind the endosymbiotic theory, that both organelles descend from free-living prokaryotes taken into an early eukaryotic cell. The theory itself is not required by any of the five specifications this site maps; the 70S ribosomes inside these organelles are examinable, because they qualify any simple statement that 70S ribosomes are found only in prokaryotes.

Ribosomes, lysosomes and the rest of the small print

Ribosomes are the exception among the organelles described so far: they have no membrane at all. Each is built from ribosomal RNA and protein in two subunits that clamp round a strand of mRNA to translate it. In the cytoplasm of a eukaryotic cell they are 80S and about 25 nm across. In prokaryotes they are 70S and smaller. The ribosomes inside mitochondria and chloroplasts are prokaryote-like too, which A-level files under 70S: close to true for chloroplasts, while mammalian mitochondrial ribosomes have been remodelled over evolutionary time and sediment nearer 55S. The S is a Svedberg unit, which measures how fast a particle settles in a centrifuge rather than its mass, which is why a 60S and a 40S subunit make an 80S ribosome instead of a 100S one.

Lysosomes are spherical sacs, roughly 0.1 to 1 µm across, each holding up to fifty kinds of hydrolytic enzyme behind a single membrane. They digest worn-out organelles, break down material taken in by phagocytosis, and in a white blood cell they empty their contents onto engulfed bacteria. The single membrane is what makes this safe. Loose in the cytoplasm those enzymes would hydrolyse the cell that made them, so they are confined to a compartment and released only at the site of digestion.

Centrioles are pairs of hollow microtubule cylinders that organise the spindle during nuclear division. They are absent from the cells of flowering plants.

Ribosome

A structure of ribosomal RNA and protein, in two subunits, with no membrane, which is the site of translation. 80S in eukaryotic cytoplasm, 70S in prokaryotes and in mitochondria and chloroplasts.

Lysosome

A vesicle containing hydrolytic enzymes, bounded by a single membrane, which digests worn-out organelles and engulfed material.

Crista

A fold of the inner mitochondrial membrane, giving a large surface area for the electron transport chain.

The cytoskeleton

Organelles are not suspended in featureless cytosol. The cytoplasm is threaded through with a network of protein fibres called the cytoskeleton, which gives the cell its shape, holds each organelle in position, and moves material, and in some cases whole cells, from place to place. Three kinds of fibre make it up, distinguished by their diameter and their protein.

Microfilaments are the thinnest, about 7 nm, built from the globular protein actin. They gather in a mesh just under the cell-surface membrane, where they let the cell change shape: a phagocyte pushing out extensions around a bacterium is rearranging its actin, and so is an animal cell in cytokinesis, where a contractile ring of microfilaments pinches the cytoplasm in two.

Intermediate filaments, around 10 nm, are the mechanical ones: tough rope-like fibres, keratins among them, that spread tension through the cell and anchor the nucleus and other organelles in position. A cell pulled about by its neighbours, as skin cells constantly are, survives because these filaments carry the load.

Microtubules are the widest at about 25 nm: hollow cylinders of the protein tubulin, constantly built and taken apart, radiating from an organising region near the nucleus that in animal cells contains the centrioles. They provide tracks for directed transport. Motor proteins, with kinesin and dynein the named examples, attach to a vesicle or an organelle and move step by step along a microtubule, each step requiring ATP. Transport and secretory vesicles are moved along microtubules by motor proteins rather than by diffusion. The spindle that moves chromosomes during nuclear division is microtubules again, organised in an animal cell by the centrioles, and in a plant cell, which has none, by the poles themselves.

Cytoskeleton

The network of protein fibres (microfilaments, intermediate filaments and microtubules) that gives a cell its shape, anchors its organelles and provides tracks for movement.

Microtubule

A hollow cylinder of tubulin about 25 nm wide, along which motor proteins move vesicles and organelles, and which builds the spindle, cilia and flagella.

Motor protein

A protein such as kinesin or dynein that uses ATP to walk along a cytoskeletal fibre, carrying a vesicle or organelle with it.

Microtubules also build the cell's moving appendages. A cilium and a eukaryotic flagellum have the same internal plan: nine pairs of microtubules arranged in a ring around two central ones, the 9 + 2 arrangement, with dynein arms between the pairs. When the dynein walks, neighbouring pairs slide against each other, and because the pairs are anchored the sliding becomes bending. A sperm flagellum and the cilia of a ciliated epithelial cell use the same internal structure at different lengths. The bacterial flagellum is a different structure: a rotating protein filament that shares only the name. Microvilli are different again: finger-like folds of the cell-surface membrane, held out by microfilaments, that increase the surface area for absorption, as on the epithelial cells of the small intestine.

Structures found in plant cells and not in animal cells

Every organelle so far appears in a plant cell too. Plant cells respire, so they have mitochondria; they make and export protein, so they have rough ER and Golgi. Four structures are added, and one is taken away.

Describe the drawing

A plant cell drawn in section as a box with rounded corners. A thick cellulose cell wall forms the outer band, pierced by narrow plasmodesmata, with the cell-surface membrane pressed against its inside. A large permanent vacuole bounded by a tonoplast fills the centre and pushes the cytoplasm into a thin layer round the edge. Four chloroplasts with stacked grana, a mitochondrion with cristae, a Golgi stack, free ribosomes and a nucleus with a nucleolus lie in that cytoplasm layer.

The cell wall is cellulose, not membrane, and that matters twice over. It is freely permeable, so it is no barrier to water or dissolved substances and cannot control what enters the cell. The cell-surface membrane still does that. And it is strong in tension, so when water enters by osmosis the wall pushes back and the cell becomes turgid rather than bursting. Turgid cells packed against each other are what holds a non-woody plant up.

The permanent vacuole is a large sac of cell sap behind a single membrane called the tonoplast. It stores water, sugars, ions and sometimes pigments, and by filling with water it keeps the cell pressed against its wall. Animal cells have vacuoles too, but small and temporary ones.

Chloroplasts are the third addition. Plasmodesmata are the fourth: narrow channels through the walls of neighbouring cells, lined with membrane, through which cytoplasm is continuous from one cell to the next. They are how a plant moves substances and signals between cells without crossing a wall.

Amyloplasts, pits and the middle lamella

Pearson Edexcel Biology A lists three more plant structures than the four above: amyloplasts, pits and the middle lamella. All three can be identified in an electron micrograph of the right tissue.

Describe the drawing

Two plastids drawn side by side as they appear in a transmission electron micrograph. On the left a lens-shaped chloroplast is bounded by two envelope membranes and holds several grana, each a stack of flattened thylakoids seen as dark parallel lines, joined by longer single membranes, with two small unshaded starch grains lying between the stacks. On the right an amyloplast of similar size is also bounded by two envelope membranes but has no thylakoids at all; one large unshaded starch grain with faint growth rings fills most of its interior, with a smaller grain beside it and a thin layer of stroma round both.

An amyloplast is a plastid that stores starch. Plastids are the family of organelles to which the chloroplast belongs, all with a double-membrane envelope, their own circular DNA and 70S ribosomes, and all developing from small undifferentiated precursors called proplastids. An amyloplast has no chlorophyll and almost no internal membrane. Its stroma holds the enzymes that build starch from glucose, made from sucrose delivered by the phloem, and one or several large starch grains take up most of its volume. Amyloplasts are found in storage tissue that receives no light, such as the tuber of a potato and the endosperm of a cereal grain, which is where the starch you eat was laid down.

A chloroplast stores starch too, but only for a short time. Starch made in the light is kept as small grains in the stroma and hydrolysed again at night, when the sugars are exported to the rest of the plant. An amyloplast is a long-term store. Amyloplasts in the cells of a root cap have a second job: their dense starch grains settle to the lower side of the cell, and that settling is one of the ways a root detects the direction of gravity. The two kinds of plastid can also convert one into the other. A potato tuber left in the light turns green at the surface as its amyloplasts develop thylakoids and chlorophyll.

The middle lamella is the layer that cements neighbouring plant cells together. It is the first layer laid down when a dividing plant cell forms a new wall, so it sits in the centre of every shared wall, with the cellulose wall of one cell on one side of it and the wall of the next cell on the other. It is made mainly of pectins, polysaccharides held together by calcium ions as calcium pectate. Dissolving it separates the cells. Ripening fruit softens partly because enzymes break down the pectins of the middle lamella, and the hydrochloric acid used in a root-tip squash works the same way, hydrolysing the middle lamella so the cells spread apart when pressed.

A pit is a thin region of a cell wall. Many plant cells, xylem among them, lay down a thick secondary wall inside the first, and a pit is a gap in that secondary wall where only the thin primary wall and the middle lamella are left. Pits in neighbouring cells usually line up, forming a pit pair, so that water and dissolved substances cross from one cell to the next through a very thin barrier. In xylem vessels, whose walls are thickened with lignin, pits are how water moves sideways between vessels. In living cells the plasmodesmata are often clustered in these thin regions.

Describe the drawing

The wall between two neighbouring plant cells drawn in section at electron microscope scale, with the cytoplasm of one cell on the left and the other on the right. Crossing from left to right, the wall is a thick secondary wall, a thin primary wall, a dark middle lamella in the centre, then a primary wall and a secondary wall belonging to the second cell. Near the top the secondary walls of both cells stop opposite each other, leaving only the primary walls and middle lamella between them: a pit pair, with each cell-surface membrane following the dip. Lower down a narrow plasmodesma runs straight through every layer, lined by membrane continuous from one cell to the other.

None of these three has an equivalent in an animal cell. Animal cells store carbohydrate as glycogen granules lying free in the cytoplasm, not inside an organelle, and they are held together by junction proteins and the extracellular matrix, not by a cementing layer between walls they do not have.

Amyloplast

A colourless plastid with a double-membrane envelope that synthesises and stores starch, found in storage tissues such as potato tubers and in root cap cells.

Middle lamella

The layer, mainly calcium pectate, between the walls of neighbouring plant cells, which cements the cells together.

Pit

A thin region of a plant cell wall where no secondary wall has been laid down, usually matched by a pit in the neighbouring cell, allowing water and solutes to pass between them.

Plastid

Any of the family of plant organelles, including chloroplasts and amyloplasts, that have a double-membrane envelope and their own DNA and develop from proplastids.

Recognising plant organelles in an electron micrograph

Pearson Edexcel Biology A asks for every plant structure in this lesson to be identified from an electron micrograph. A transmission electron micrograph is a black-and-white image of a thin section, so identification depends on shape, size, the number of membranes and what lies inside them, not on colour.

Amyloplast and chloroplast are the pair most often confused, because both are plastids with a double envelope and both can contain starch. Decide on the internal membranes. Grana, seen as dark stripes in stacks, mean a chloroplast however much starch is present. No grana and a starch grain occupying most of the organelle mean an amyloplast. The tissue the cell came from is supporting evidence only: a leaf mesophyll cell holds chloroplasts and a cell from a potato tuber holds amyloplasts.