1The idea in one paragraph

Every living thing is made of cells, and every cell has the same three basics: DNA as its genetic material, a cytoplasm that is mostly water, and a plasma membrane of lipids around it. On that plan there are two designs. Prokaryotic cells, the bacteria and archaea, are small and simple: their DNA is a loop lying in the cytoplasm, with no nucleus and no membrane-bound organelles. Eukaryotic cells, the cells of animals, plants, fungi and protists, are larger and divided into compartments: a nucleus holds the DNA, and organelles such as mitochondria, the endoplasmic reticulum and the Golgi apparatus each do a job. We know all this because of microscopes: light microscopes show cells, and electron microscopes show what is inside them. At HL, the story adds where eukaryotic cells came from, by one cell taking up another, and how multicellular organisms make many kinds of cell from one set of genes.

2Cell theory, and what it lets you predict

Cell theory states that cells are the basic structural unit of all living organisms: every organism is made of one or more cells, and nothing smaller than a cell is alive in its own right. (Cells only come from pre-existing cells, which A2.1 explored at HL.)

Nature of science: deduction from a theory. A theory is useful because it predicts. Reasoning from a general principle to a particular case is deductive reasoning: if all living organisms consist of cells, and this is a newly discovered living organism, then it will consist of one or more cells. A biologist who finds a new organism in a deep-sea sediment does not need to wonder whether it is made of cells; the theory predicts it, and the microscope can then test the prediction. If the prediction ever failed, the theory would be in trouble.

3Microscopy skills

The guide expects you to have done these things yourself, and exam questions test whether you understand them.

Temporary mounts. A thin layer of cells or tissue is placed in a drop of water or stain on a glass slide and covered with a cover slip, lowered at an angle to avoid trapping air bubbles. Thin, so light can pass through; one layer of cells, so they do not overlap.

Staining. Most cells are almost transparent. A stain binds to some structures more than others and gives contrast: iodine solution stains starch blue-black, and methylene blue makes the nuclei of animal cells stand out.

Focusing. Start with the lowest-power objective lens. Use the coarse focus knob to bring the image roughly into view, then the fine focus knob to sharpen it. At high power use only the fine focus, so the lens does not crash into the slide.

Measuring with an eyepiece graticule. A graticule is a small scale in the eyepiece. It has no units of its own, because what one division covers depends on the objective lens in use. So it must be calibrated against a stage micrometer, a slide with a scale of known size, usually 1 mm divided into 100 divisions of 10 µm each. Figure 1 shows the method.

Change the objective and you must recalibrate. Measuring is a quantitative observation (nature of science): an instrument turns a look into a number, which can be compared, averaged and checked by someone else. It also brings uncertainty. Each reading is only as good as the smallest division, so measure several cells and take a mean.

Magnification and actual size. The one formula to learn:

magnification = size of image ÷ actual size of the specimen

It rearranges to actual size = image size ÷ magnification. The only trap is units: both sizes must be in the same unit before you divide. Work in micrometres.

A mitochondrion in an electron micrograph measures 36 mm, and the magnification is ×12,000.

Scale bars. A scale bar is a line on a micrograph or drawing labelled with the actual length it represents. It stays correct if the image is enlarged or shrunk, which a written magnification does not. To find magnification from one, measure the bar with a ruler and divide by what it represents. A bar labelled 5 µm that measures 20 mm:

To produce a scale bar for your own drawing, choose a round actual length, such as 10 µm, and multiply it by the magnification to find how long to draw the line.

Taking photographs. A phone camera held to the eyepiece, or a camera attached to the microscope, records what you saw. A photograph (a micrograph) is evidence other people can check, but it still needs a scale bar or a stated magnification to be useful.

4Developments in microscopy

A light microscope can magnify further than about ×1,500, but the extra size shows no extra detail. What limits it is resolution: the smallest distance between two points that can still be seen as separate. For light it is about 0.2 µm, set by the wavelength of light. Figure 2 shows what that means for the things biologists want to see.

Electron microscopy. An electron microscope uses a beam of electrons, whose wavelength is far shorter than that of light, so its resolution is far better: detail of around 1 nm in biological specimens, some 200 times finer. That revealed the ultrastructure of cells: ribosomes, the membranes of the endoplasmic reticulum, the inner folds of mitochondria, none of which a light microscope can resolve. The trade-offs: specimens must be in a vacuum and so are dead, images are black and white (colour in published images is added), and the equipment is large and expensive.

The guide names four further developments.

• Freeze fracture. A specimen is frozen very rapidly and then cracked with a blade. The crack tends to run along the middle of membranes, splitting the two layers of the bilayer apart and exposing the inside of the membrane. A replica of the surface is made and viewed in the electron microscope. It showed particles, proteins, embedded right through the membrane, which was key evidence for the fluid mosaic model (B2.1).
• Cryogenic electron microscopy (cryo-EM). Samples are frozen so fast in a thin film of water that ice crystals cannot form and damage them, then imaged at very low temperature. Computers combine many images of individual molecules into a three-dimensional structure. It lets scientists see the shapes of proteins and viruses close to atomic detail without having to make crystals of them; its developers shared the 2017 Nobel Prize in Chemistry.
• Fluorescent stains in light microscopy. A dye that glows when lit with light of a particular wavelength binds to one kind of structure, for example DNA, so that structure shines brightly against a dark background.
• Immunofluorescence. An antibody binds to one specific protein and nothing else. Attach a fluorescent marker to the antibody and you can see exactly where that protein is in a living or preserved cell. Using several antibodies with different colours shows several proteins at once.

5What every cell has

Look at any cell from any organism and three structures are always there. The guide wants the reasons, not just the list.

• DNA as the genetic material. Every cell needs instructions for making its proteins, and must pass them to its daughter cells. DNA is stable and can be copied accurately (A1.2).
• A cytoplasm composed mainly of water. Metabolism happens in solution: substrates and enzymes must be dissolved to move and collide (A1.1).
• A plasma membrane composed of lipids. A barrier is needed to keep the cell's contents in and to control what enters and leaves. Lipids are hydrophobic, so a lipid bilayer stops water-soluble substances from crossing freely, which is what lets the inside of a cell differ from the outside.

These three are the unity in "unity and diversity". Everything else varies.

6Prokaryotic cells

Prokaryotes are the bacteria and archaea. The guide asks for the structure of a Gram-positive eubacterium such as Bacillus or Staphylococcus, shown in Figure 3.

• Cell wall. Outside the membrane, it keeps the cell's shape and stops it bursting when water enters by osmosis. In Gram-positive bacteria it is thick.
• Plasma membrane. Controls what enters and leaves.
• Cytoplasm. Where all the cell's metabolism happens, since there are no organelles to divide the work.
• Naked DNA in a loop. A single circular chromosome, not associated with histones, lying in a region of the cytoplasm called the nucleoid. There is no nuclear membrane.
• 70S ribosomes. Smaller than those of eukaryotes (the S is a measure of size, from how fast a particle sinks in a centrifuge), free in the cytoplasm.

Prokaryote structure varies, and you should know that it does, though you are not required to learn the variations. The key comparison is the absence: no nucleus and no membrane-bound organelles.

7Eukaryotic cells

Eukaryotic cells are larger, typically 10–100 µm, and their cytoplasm is compartmentalised: divided by membranes into separate spaces, each suited to a job. Figure 4 shows an animal cell as the electron microscope sees it.

The features common to eukaryotic cells, as the guide lists them:

• A plasma membrane enclosing a compartmentalised cytoplasm with 80S ribosomes.
• A nucleus containing chromosomes made of DNA bound to histones, enclosed in a double membrane with pores.
• Membrane-bound organelles: mitochondria; endoplasmic reticulum, rough (with ribosomes) and smooth; the Golgi apparatus; and a variety of vesicles and vacuoles, including lysosomes.
• A cytoskeleton of microtubules and microfilaments, which gives shape and moves things around the cell.

Compartments matter because different reactions need different conditions. Lysosomes hold digestive enzymes that would destroy the rest of the cell if they were loose; the nucleus keeps DNA apart from the busy cytoplasm; mitochondria concentrate the enzymes of aerobic respiration.

8Life in a single cell

A unicellular organism is one cell that must carry out every function of life by itself. The guide lists eight, and two freshwater organisms show them well: Paramecium, a heterotroph that swims with cilia, and Chlamydomonas, a photosynthetic alga with two flagella.

In a multicellular organism these jobs are shared out between specialised cells. In a unicellular organism, one cell does them all.

9Animals, fungi and plants

All three are eukaryotes, but their cells differ in the four ways the guide names. Figure 5 is a plant cell to set beside the animal cell in Figure 4.

A wall stops a cell bursting when it takes in water, which is why plants and fungi, which rely on water pressure for support, have one and animals do not. A plant's sap vacuole filled with water pushes the cytoplasm against the wall and keeps the cell turgid. Chloroplasts are where photosynthesis happens, so only photosynthetic cells need them; a root cell has none.

10Atypical eukaryotic cells

The usual eukaryotic cell has one nucleus. The guide uses numbers of nuclei to show that some cells break the rule, and Figure 6 draws its four examples.

• Aseptate fungal hyphae: many nuclei. Fungal hyphae are thread-like filaments. In aseptate fungi there are no cross-walls (septa) dividing them into cells, so one long, continuous cytoplasm contains many nuclei.
• Skeletal muscle fibres: many nuclei. Each fibre forms when many cells fuse, so it is very long and has many nuclei. A single contracting unit that long works better than a chain of separate cells.
• Red blood cells: no nucleus. Mammalian red blood cells lose their nucleus as they mature. That leaves more room for haemoglobin, so each cell carries more oxygen, but it also means they cannot divide or repair themselves, and they live only a few months.
• Phloem sieve tube elements: no nucleus. They lose their nucleus and most organelles, leaving an open tube through which sap flows easily. Each depends on an adjacent companion cell, which has a nucleus, to keep it alive.

Why call them atypical rather than "not cells"? Each still has a membrane, cytoplasm and a clear origin from normal cells, but its structure departs from the one-nucleus plan, usually because of its function.

11Reading micrographs and drawing from them

Identifying cells. In a micrograph, decide first whether a cell is prokaryotic, plant or animal. Prokaryote: very small, no nucleus, a wall. Plant: a regular shape with a wall, a large vacuole, chloroplasts in green tissue. Animal: no wall, an irregular outline, no large vacuole.

Identifying structures in electron micrographs. The guide lists the structures you must recognise. What each looks like:

Drawing and annotating. The guide asks you to draw organelles (nucleus, mitochondria, chloroplasts, sap vacuole, Golgi apparatus, rough and smooth ER, chromosomes) and other structures (cell wall, plasma membrane, secretory vesicles, microvilli) from electron micrographs, with functions in the annotations. Figure 7 shows four done properly.

An annotation is a label plus a note of what the part does. The functions to have ready:

• Nucleus: holds the chromosomes; site of DNA replication and transcription; nuclear pores let mRNA out.
• Mitochondrion: aerobic respiration, producing ATP; cristae give a large area for the membrane-bound stages.
• Chloroplast: photosynthesis; the thylakoid membranes absorb light, the stroma makes sugar.
• Sap vacuole: stores water, ions and other solutes; keeps the cell turgid.
• Golgi apparatus: modifies, sorts and packages proteins, sending them off in vesicles.
• Rough ER: its ribosomes make proteins for secretion or for membranes, which pass into the ER to be transported.
• Smooth ER: makes lipids, including phospholipids and steroids.
• Chromosomes: carry the genes; condensed so they can be separated when the cell divides.
• Cell wall: support; resists bursting.
• Plasma membrane: controls entry and exit of substances.
• Secretory vesicles: carry proteins to the membrane, where they are released by exocytosis.
• Microvilli: increase the surface area of the membrane for absorption, as in the lining of the small intestine.