Eukaryotic Cells and Their Organelles

A eukaryotic cell is a cell with a nucleus and membrane-bound organelles: every plant, animal, fungus and protoctist is made of them. Each organelle is a compartment with a particular job, and the cell works because those compartments cooperate. This note covers every organelle on the syllabus, how to recognise each one in electron micrographs, how plant and animal cells differ, and the route a protein takes from gene to secretion. Organelle identification and "outline the structure and function" questions appear on almost every Paper 1 and Paper 2.

Two kinds of cell

All cells are either prokaryotic (bacteria, with no nucleus) or eukaryotic (with a nucleus). The word means "true nucleus". Eukaryotic cells are typically 10–100 µm across, much larger than bacteria (1–5 µm), and are divided internally by membranes into organelles: structures with a specific function inside a cell. Compartmentalisation lets incompatible reactions run side by side (the digestive enzymes of a lysosome are kept away from the rest of the cytoplasm, for example) and gives large areas of membrane on which enzymes can be arranged.

The bacterial cell is compared with eukaryotic cells in Prokaryotes and viruses.

What you can see with each microscope

With a light microscope, a typical animal cell shows a cell surface membrane (as the outline of the cell), cytoplasm, a nucleus, and sometimes a nucleolus and mitochondria as tiny dots. A plant cell additionally shows a cell wall, chloroplasts and a large vacuole.

The internal detail of organelles, and all the small ones (ribosomes, ER, Golgi body, lysosomes, centrioles), is known as the cell's ultrastructure and can only be seen with an electron microscope, because they are smaller than the 200 nm resolution limit of the light microscope (see Microscopy).

The organelles one by one

Cell surface membrane

Structure. A phospholipid bilayer about 7–10 nm thick with proteins, cholesterol, glycolipids and glycoproteins (the fluid mosaic model). In electron micrographs at high magnification it appears as two dark lines with a pale line between them (the "railway track" appearance).

Function. It is partially permeable, controlling which substances enter and leave the cell. Its proteins act as channels, carriers, receptors for cell signalling and antigens for cell recognition. The details are in The fluid mosaic model.

Nucleus, nuclear envelope and nucleolus

Structure. The largest organelle, usually about 10 µm across. It is surrounded by the nuclear envelope, two membranes separated by a narrow space. The outer membrane is continuous with the rough endoplasmic reticulum and often has ribosomes on it. The envelope is perforated by nuclear pores. Inside is chromatin, the DNA wound around histone proteins, which condenses into visible chromosomes only when the cell divides. Dense, darkly staining chromatin is heterochromatin; the lighter, more open chromatin is euchromatin, which is being transcribed. The nucleolus is a dense, darker region (not membrane-bound) inside the nucleus.

Function.

• The nucleus contains the cell's genetic information as DNA, and so controls the activities of the cell by controlling which proteins are made.
• DNA is replicated and transcribed (to make mRNA) in the nucleus.
• Nuclear pores allow mRNA and ribosomal subunits to leave the nucleus, and allow molecules such as nucleotides, ATP and some proteins (such as DNA polymerase and histones) to enter.
• The nucleolus makes ribosomal RNA (rRNA) and assembles ribosomal subunits.

Rough endoplasmic reticulum (RER)

Structure. A network of flattened membrane-bound sacs called cisternae, continuous with the outer nuclear membrane, with ribosomes attached to the outer surface, which gives the "rough" appearance in electron micrographs.

Function. Its ribosomes make proteins that are destined for secretion (such as digestive enzymes and peptide hormones), for insertion into membranes, or for lysosomes. As each polypeptide is made it passes into the cisternal space, where it folds and may be modified. The RER then transports the protein through its cisternae and buds off vesicles that carry it to the Golgi body.

Smooth endoplasmic reticulum (SER)

Structure. A network of membrane-bound tubules and sacs with no ribosomes, so it looks smooth and more tubular than the RER.

Function. Synthesis and transport of lipids, including phospholipids and cholesterol, and steroids such as the steroid hormones (for example, oestrogen and testosterone). In liver cells the SER contains enzymes that detoxify drugs and poisons. In muscle cells a specialised SER (the sarcoplasmic reticulum) stores calcium ions.

Golgi body (Golgi apparatus or Golgi complex)

Structure. A stack of flattened, curved membrane-bound sacs (cisternae), not connected to each other, with many small vesicles around the edges. In micrographs it looks like a stack of curved pancakes with bubbles at the ends.

Function. It receives proteins (and lipids) from the ER in vesicles, which fuse with the stack on one side. It then modifies them, for example adding carbohydrate to make glycoproteins, or removing part of a polypeptide to activate it. It sorts and packages them into vesicles: secretory vesicles, which move to the cell surface membrane and release their contents by exocytosis; and lysosomes. It also makes the polysaccharides of plant cell walls.

Mitochondria

Structure. Usually about 0.5–1 µm wide and 1–10 µm long. A double membrane (the envelope) surrounds the organelle. The inner membrane is folded into cristae, giving it a large surface area. The fluid inside is the matrix, which contains enzymes, 70S ribosomes and small circular DNA.

Function. The site of aerobic respiration, producing ATP. The Krebs cycle takes place in the matrix; the electron transport chain and ATP synthase are on the inner membrane, so more cristae means more ATP production. The circular DNA and 70S ribosomes allow mitochondria to make some of their own proteins. Cells with high energy demands, such as muscle cells, sperm cells, liver cells and cells carrying out active transport, have many mitochondria with densely packed cristae.

Ribosomes

Structure. Tiny (about 20–30 nm) non-membrane-bound organelles made of ribosomal RNA (rRNA) and protein, in two subunits, one large and one small. They appear as small dark dots in electron micrographs. Ribosomes are described by their size in S units (Svedberg units, a measure of how fast they sediment in a centrifuge):

• 80S ribosomes are found in the cytoplasm of eukaryotic cells, either free or attached to the RER.
• 70S ribosomes are found in mitochondria and chloroplasts (and in prokaryotes).

Function. The site of protein synthesis (translation): the ribosome holds the mRNA and tRNA in place while amino acids are joined by peptide bonds. Free ribosomes make proteins used within the cytoplasm (such as glycolysis enzymes); ribosomes on the RER make proteins for secretion, membranes or lysosomes.

Lysosomes

Structure. Spherical vesicles about 0.1–0.5 µm across, surrounded by a single membrane, containing hydrolytic (digestive) enzymes such as proteases, lipases and nucleases. They have no internal structure and appear as dark, uniformly stained circles. They are made by the Golgi body.

Function. Digestion (hydrolysis) of unwanted material:

• breaking down worn-out organelles inside the cell (autophagy) so that their components can be reused;
• digesting material taken into the cell by phagocytosis, for example bacteria engulfed by a phagocyte, when the lysosome fuses with the phagocytic vacuole;
• releasing enzymes outside the cell (exocytosis), as in the acrosome of a sperm cell;
• destroying the whole cell (autolysis) when it is no longer needed.

The membrane keeps the enzymes separate from the rest of the cell, so they do not digest the cell's own components.

Centrioles and microtubules

Microtubules are long, straight, hollow tubes about 25 nm in diameter, made of the globular protein tubulin. They are part of the cytoskeleton, a network of protein fibres that supports the cell and determines its shape. Microtubules also act as tracks along which organelles and vesicles are moved (using ATP), make up the spindle that moves chromosomes in nuclear division, and form the internal structure of cilia and flagella.

Centrioles are found in animal cells (and many protoctists) but not in the cells of flowering plants. They occur as a pair at right angles to each other, close to the nucleus, in a region called the centrosome. Each centriole is a hollow cylinder about 0.5 µm long made of nine triplets of microtubules.

The centrosome acts as a microtubule organising centre: in animal cells the spindle microtubules grow out from it during cell division. Centrioles are not essential for making a spindle, since plant cells divide without them. Centrioles also form the basal bodies at the base of cilia and flagella.

Cilia

Structure. Hair-like extensions of the cell surface, about 0.25 µm in diameter and up to about 10 µm long, enclosed by the cell surface membrane. Each contains a ring of nine pairs of microtubules surrounding two central microtubules (the "9 + 2" arrangement), anchored by a basal body. In cross-section in an electron micrograph this pattern is distinctive.

Function. Cilia beat in a coordinated, wave-like way, using ATP, to move fluid or mucus over the cell surface. Ciliated epithelium in the trachea and bronchi moves mucus (with trapped dust and bacteria) up to the throat; cilia in the oviduct move an egg towards the uterus.

Microvilli

Structure. Finger-like folds (extensions) of the cell surface membrane, about 1 µm long and about 0.1 µm wide, much smaller than cilia and without the 9 + 2 microtubules (they contain actin filaments). Seen in electron micrographs as a fringe called a brush border.

Function. They greatly increase the surface area of the cell surface membrane for absorption, for example in the epithelial cells of the small intestine (absorbing digested food) and the proximal convoluted tubule of the kidney (reabsorption). They do not move.

Chloroplasts

Structure. Found in some plant cells (for example, palisade and spongy mesophyll and guard cells) and algae. Usually lens-shaped, about 3–10 µm long. A double membrane (envelope) surrounds a fluid stroma. Inside is a system of flattened membrane sacs called thylakoids, stacked into grana (singular granum) and linked by intergranal lamellae. The stroma contains enzymes, starch grains, lipid droplets, 70S ribosomes and small circular DNA.

Function. The site of photosynthesis. Chlorophyll and other pigments on the thylakoid membranes absorb light for the light-dependent reactions; the stroma is the site of the light-independent reactions (the Calvin cycle), which fix carbon dioxide into sugars. Starch is a store of the sugars made. Like mitochondria, chloroplasts make some of their own proteins using their own DNA and 70S ribosomes.

Cell wall

Structure. Found outside the cell surface membrane of plant cells. Made of cellulose microfibrils embedded in a matrix of other polysaccharides. A thin, flexible primary wall is laid down first; some cells (such as xylem vessels) add a thick secondary wall, often strengthened with lignin. Neighbouring cells are cemented together by the middle lamella. The walls of fungi are made of chitin, and those of bacteria of peptidoglycan.

Function.

• Gives mechanical strength and support to the cell and to the plant.
• Prevents the cell bursting when water enters by osmosis, allowing the cell to become turgid, which supports non-woody plants.
• Is fully (freely) permeable to water and solutes, so it allows water and dissolved substances to move through and between cells (the apoplast pathway).
• Determines the shape of the cell.

Plasmodesmata

Structure. Narrow channels (about 40 nm wide) through the cell walls of adjacent plant cells, lined with cell surface membrane, so that the cytoplasm of one cell is continuous with the cytoplasm of the next. A thin tube of ER (the desmotubule) passes through the centre.

Function. They allow communication and the movement of substances, such as water, sugars, ions and some signalling molecules, between the cytoplasm of neighbouring cells. This is the symplast pathway, important in water movement across the root and in loading the phloem.

Large permanent vacuole and tonoplast

Structure. Mature plant cells usually have a single large vacuole filling much of the cell, surrounded by a partially permeable membrane called the tonoplast. It contains cell sap: a solution of water, sugars, mineral ions, amino acids, waste substances and sometimes pigments (such as the anthocyanins in red cells). Animal cells may have small, temporary vacuoles (such as phagocytic vacuoles), never a large permanent one.

Function.

• Water entering the vacuole by osmosis pushes the cytoplasm against the cell wall, making the cell turgid and supporting the plant.
• The tonoplast controls what enters and leaves the vacuole, so the vacuole helps regulate the water potential of the cell.
• Storage of sugars, ions and pigments; some vacuoles contain hydrolytic enzymes and act like lysosomes.
• Storage of waste or toxic compounds that deter herbivores.

Summary table of organelles

Notice the pattern of membranes: the double-membrane structures are the nucleus, mitochondria and chloroplasts. The single-membrane structures are ER, Golgi body, lysosomes, vesicles and vacuoles. The non-membrane-bound structures are ribosomes, centrioles, microtubules and the nucleolus.

How a secretory protein is made and released

The organelles involved in protein secretion work as a production line. This sequence is examined often, and each step must be in the right organelle.

Comparing plant and animal cells

Feature	Typical plant cell	Typical animal cell
Cell wall	present (cellulose)	absent
Plasmodesmata	present	absent
Chloroplasts	present in many cells (e.g. mesophyll)	absent
Vacuole	large permanent vacuole with tonoplast	only small, temporary vacuoles
Centrioles	absent (in flowering plants)	present
Cilia and microvilli	absent (in flowering plants)	present in some cells
Carbohydrate store	starch grains	glycogen granules
Shape	usually regular, fixed by the wall	variable, often rounded
Position of nucleus	often pushed to the edge by the vacuole	usually central
Lysosomes	rare (vacuole takes their role)	common

Both have: cell surface membrane, nucleus with nuclear envelope and nucleolus, rough and smooth ER, Golgi body, mitochondria, 80S ribosomes in the cytoplasm, microtubules.

Interpreting electron micrographs

Questions give you a transmission electron micrograph and ask you to identify labelled structures, often with a twist (a cell type you have not seen before). Work from these clues:

If you see ...	It is probably ...
a large round structure with a double membrane and pores, containing darker patches	nucleus (dark patches are heterochromatin; the darkest round area is the nucleolus)
a sausage or oval shape with a double membrane and inner folds	mitochondrion (folds are cristae)
a large oval with stacks of membranes inside, often with pale starch grains	chloroplast (stacks are grana)
parallel membranes covered with dots	rough ER
a stack of curved membranes with vesicles at the edges, no dots	Golgi body
small round dark circles with no internal structure	lysosomes (or vesicles)
tiny dark dots scattered through the cytoplasm	free ribosomes
a pair of small cylinders, one cut lengthways and one across	centrioles
a fringe of tiny projections on one surface	microvilli
long projections with a 9 + 2 ring of tubules in cross-section	cilia
a thick pale layer outside the membrane	cell wall

Practice questions

Answers

1. (a) Lysosome. (b) Nucleolus. (c) Chloroplast (stroma). (d) Smooth endoplasmic reticulum.
2. Plant only: any three of cell wall, plasmodesmata, chloroplasts, large permanent vacuole (with tonoplast), starch grains. Animal only: centrioles (or cilia, microvilli, glycogen granules).
3. Double membrane (envelope); inner membrane folded into cristae; matrix (inside the inner membrane) containing 70S ribosomes, circular DNA (and granules).
4. S units measure size (how fast a particle sediments in a centrifuge). Cytoplasmic ribosomes of eukaryotes are larger (80S); mitochondria have smaller 70S ribosomes, like those of prokaryotes. (Background: evidence for the endosymbiont theory.)
5. Cilia: larger (up to about 10 µm long), contain microtubules in a 9 + 2 arrangement, have a basal body, beat (using ATP) to move fluids or mucus. Microvilli: smaller (about 1 µm), folds of the cell surface membrane without microtubules, do not move, increase surface area for absorption.
6. The nuclear envelope (double membrane) separates the DNA from the cytoplasm, protecting it and allowing transcription to be controlled; nuclear pores allow mRNA and ribosomal subunits out to the cytoplasm and let nucleotides, enzymes and other molecules in.
7. The bacterium is enclosed in a phagocytic vacuole; lysosomes (made by the Golgi body) fuse with the vacuole and release hydrolytic enzymes into it; the enzymes hydrolyse (digest) the bacterium; soluble products are absorbed into the cytoplasm.
8. Many mitochondria (with many cristae) to supply ATP for active transport; many ribosomes or extensive RER to make carrier proteins for the cell surface membrane; also a large surface area of cell surface membrane (the hair), no chloroplasts.
9. Gene in nucleus transcribed to mRNA; mRNA leaves via nuclear pores; translated by ribosomes on RER; polypeptide enters RER cisternae, folds, transported; vesicles bud off and carry it to Golgi body; Golgi body adds carbohydrate (forms the glycoprotein) and packages it; secretory vesicles move to and fuse with the cell surface membrane; exocytosis; ATP from mitochondria.
10. The conclusion is not valid: many plant cells, such as root cells and cells deep in a stem, have no chloroplasts. The presence of a cell wall and large permanent vacuole indicates a plant cell (fungal cells also have walls and vacuoles, so check further). To identify it: test the wall for cellulose (plant) versus chitin (fungus); look for plasmodesmata and starch grains (plant) and for the absence of centrioles.