Pearson Edexcel International A Level Biology: Cell Ultrastructure and Microscopy (YBI11)

Here the focus is the Pearson Edexcel International A Level Biology (YBI11) specification, Issue 2, which covers both AS and A2 stages. The guide deals with statements 3.1 to 3.8 of Topic 3 (Cell Structure, Reproduction and Development), with Core Practical 5 included. Topics 1 to 4 sit in the International AS (IAS) half of the qualification, so you meet this material at IAS stage. Nothing here is tiered.

Use it with the revision notes and the practice questions. The course hub is at Edexcel A Level Biology, the printable list is the checklist, and the free diagnostics show where to start. Related pages: membranes and gas exchange and the exam preparation guide.

Scope and statements

Statement	Outcome
3.1	Know all living organisms are made of cells with common features
3.2	Explain how cells form tissues, tissues organs, organs organ systems
3.3 (i)(ii)	Know the ultrastructure and function of eukaryotic organelles
3.4	Explain the roles of rER and Golgi in protein transport and extracellular enzymes
3.5 (i)(ii)	Know the ultrastructure and function of prokaryotic structures
3.6	Recognise the organelles in 3.3 from electron microscope (EM) images
3.7 (i)(ii)	Know how magnification and resolution are achieved with light and electron microscopy, and why specimens are stained
3.8 (Core Practical 5)	Make observations and labelled drawings of animal cells with a light microscope; use a graticule to measure and understand scale

3.1 Cells are the common unit of life

Every living organism is made of one or more cells. Cells share common features: they are surrounded by a cell surface membrane, they contain genetic material (DNA), they have cytoplasm in which the chemical reactions of metabolism take place, and they make proteins on ribosomes. Both prokaryotic cells and eukaryotic cells show all of these. What differs is how the contents are organised.

3.2 Cells, tissues, organs and organ systems

Specialised cells are arranged into a hierarchy.

• A tissue is a set of similar cells that share one job, for example squamous epithelium lining an alveolus.
• An organ is made of several tissues working together, for example the stomach (epithelium, muscle, connective tissue, nerve tissue).
• An organ system is a group of organs that together carry out a major function, for example the digestive system.

Explanations should always name the tissues. “The stomach contains muscle tissue, whose contraction churns the food” earns more than “the stomach has different cells”.

3.3 Ultrastructure of eukaryotic cells

Ultrastructure means detail seen only with an electron microscope. Eukaryotic cells have their DNA enclosed in a nucleus and have membrane-bound organelles.

Organelle	Ultrastructure	Function
Nucleus	Surrounded by a double membrane (nuclear envelope) with pores; contains chromatin	Holds DNA; transcription; pores let mRNA leave
Nucleolus	Dense region inside the nucleus	Makes ribosomal RNA and assembles ribosome subunits
Ribosomes	Tiny, no membrane; free in cytoplasm or on rER	Site of translation (protein synthesis)
Rough endoplasmic reticulum (rER)	Flattened sacs (cisternae) continuous with the nuclear envelope, studded with ribosomes	Folds and processes proteins made on its ribosomes
Smooth endoplasmic reticulum (sER)	Tubular membranes, no ribosomes	Makes and stores lipids; processes carbohydrates
Mitochondria	Double membrane; inner membrane folded into cristae; fluid matrix	Site of the later stages of aerobic respiration; makes ATP
Centrioles	Two short hollow cylinders of microtubules at right angles	Form the spindle used in nuclear division
Lysosomes	Small round sacs with a single membrane	Contain hydrolytic enzymes that break down worn-out organelles and material taken in
Golgi apparatus	Stack of flattened membrane sacs with vesicles at the edges	Modifies, packages and sorts proteins and lipids

Learn each organelle with all three parts: where it is, what it looks like, what it does. Mitochondria are a favourite: the large surface area of the cristae gives room for the enzymes of the electron transport chain.

3.4 Protein transport: rER, Golgi and extracellular enzymes

Proteins that leave the cell, such as digestive enzymes, follow a fixed route.

1. The gene is transcribed in the nucleus; mRNA leaves through a nuclear pore.
2. Ribosomes on the rER translate the mRNA. The new polypeptide passes into the rER lumen, where it folds.
3. Vesicles pinch off the rER, carrying the protein to the Golgi apparatus.
4. The Golgi modifies the protein (for example adding carbohydrate) then wraps it in secretory vesicles.
5. Vesicles move to the cell surface membrane, fuse with it and release the contents by exocytosis. An enzyme released this way is an extracellular enzyme.

Lysosomes also form at the Golgi, which is why they contain enzymes made on the rER. Proteins made on free ribosomes stay in the cytoplasm.

3.5 Ultrastructure of prokaryotic cells

Prokaryotic cells have no nucleus and no membrane-bound organelles. They are usually much smaller than eukaryotic cells; a typical bacterium such as E. coli is around 2 micrometres long.

Structure	Function
Cell wall	Rigid layer outside the membrane; protects the cell and prevents bursting in dilute surroundings
Capsule	Slimy layer outside the wall; protects from drying and from attack by cells of the immune system, and helps cells stick
Plasmid	Small loop of DNA separate from the main chromosome; often carries genes such as antibiotic resistance
Flagellum	Long protein filament that rotates to move the cell
Pili	Short hair-like protein fibres; attach cells to surfaces and, in some bacteria, link cells for DNA transfer
Ribosomes	Translation; smaller (70S) than eukaryotic cytoplasmic ribosomes (80S)
Circular DNA	The main chromosome: a loop of DNA, not wrapped around histones in a nucleus, holding the cell’s genes

Not every bacterium has a capsule, a flagellum or plasmids, so describe them as structures that may be present.

3.6 Recognising organelles in EM images

Electron micrographs are black and white. Look for the following.

• Nucleus: a large rounded structure with a double boundary broken by pores and dark patches of chromatin; the nucleolus is the darkest region.
• Mitochondria: oval or sausage shapes with a double boundary and an inner membrane folded into cristae. A cut through one may look round.
• rER: stacked flattened sacs with dark dots (ribosomes) on the outside. sER looks similar but has no dots.
• Golgi apparatus: a curved stack of flat sacs with small vesicles at the ends.
• Lysosomes: small, round, dark and uniform, with one boundary membrane.
• Ribosomes: very small dark dots.

A section is a thin slice, so one organelle can appear as different shapes. Judge by membrane count and internal detail, not outline alone.

3.7 Magnification, resolution and staining

Magnification is the number of times an image is bigger than the specimen. Resolution is the least separation at which two neighbouring points still appear as two. A magnified image that is blurred has high magnification and poor resolution.

	Light microscope	Electron microscope
Radiation	Visible light	Beam of electrons
Resolution	About 0.2 micrometres	Far better, well below 1 nanometre in the best instruments
Specimen	Can be living	Dead; placed in a vacuum
Image	Colour possible	Black and white

How each is achieved. A light microscope uses glass lenses: the objective forms an enlarged image that the eyepiece enlarges again, so total magnification = objective magnification × eyepiece magnification. An electron microscope uses electromagnets to focus the beam of electrons on the specimen. In both cases resolution depends on the radiation used, and extra magnification cannot add detail.

Resolution is limited by wavelength. Electrons have a much shorter wavelength than light, so an electron microscope resolves much finer detail. A transmission electron microscope (TEM) shows thin sections and so the internal ultrastructure. A scanning electron microscope (SEM) shows surfaces in three dimensions. Increasing magnification beyond the resolution just enlarges blur.

Staining (3.7 ii). Most cell structures are almost transparent, so there is little contrast. A stain binds to certain structures and makes them visible. Methylene blue stains nuclei in animal cells; iodine solution stains starch. Electron microscopy uses heavy metal stains that scatter electrons and so give contrast.

The magnification formula

magnification = size of image ÷ size of real object

Use the same unit for both sides (1 mm = 1000 micrometres; 1 micrometre = 1000 nm).

Worked example 1. A cheek cell nucleus measures 21 mm on a photomicrograph. Its real diameter is 7 micrometres. Convert 21 mm to 21 000 micrometres. Magnification = 21 000 ÷ 7 = ×3000.

Worked example 2. A student’s drawing of a white blood cell measures 36 mm and the drawing is at ×900. Rearranging the formula, real size = image size ÷ magnification = 36 000 micrometres ÷ 900 = 40 micrometres.

Worked example 3 (scale bar). An electron micrograph has a scale bar 25 mm long labelled 2 micrometres. Magnification = 25 000 ÷ 2 = ×12 500. A mitochondrion measures 38 mm. Real length = 38 ÷ 25 × 2 = 3.04 micrometres, or about 3.0 micrometres.

3.8 Core Practical 5: light microscope work

(i) Observations and labelled drawings. Suitable animal cells include cheek epithelial cells, stained with methylene blue, or a prepared blood smear.

1. Place a thin smear on a slide, add stain, lower the coverslip slowly from one edge so that bubbles are not trapped.
2. Start on the lowest power objective, focus with the coarse knob, then the fine knob; move up to higher power only after centring the cells.
3. Draw with a sharp pencil, in clear continuous lines, no shading and no colouring. Draw a few cells, large, with label lines that do not cross, each ending exactly on the structure.
4. Add a title and the magnification.

(ii) Graticule and scale. An eyepiece graticule is a ruler in the eyepiece with arbitrary divisions. It must be calibrated for each objective lens using a stage micrometer, a slide with a scale of known size.

Worked example 4. At ×400 the 100 graticule divisions line up with 40 divisions on a stage micrometer, each division 10 micrometres.

• Length covered = 40 × 10 = 400 micrometres.
• One graticule division = 400 ÷ 100 = 4.0 micrometres.
• A cell 9 divisions long is 9 × 4.0 = 36 micrometres.

At a lower power the same graticule would show each division as a larger distance, so the calibration must be repeated whenever the objective changes.

Common errors

• Writing “mitochondria produce energy”. Say they make ATP by aerobic respiration.
• Using magnification and resolution as if they mean the same thing.
• Mixing units in a magnification calculation.
• Saying prokaryotes have “no DNA”, rather than DNA that is circular and not enclosed in a nucleus.
• Describing a bacterial cell wall as cellulose. Bacterial walls are not made of cellulose, so give the function, not a guessed composition.
• Forgetting that electron microscope specimens are dead.

Official syllabus

Pearson Edexcel International Advanced Subsidiary/Advanced Level in Biology (YBI11), Specification, Issue 2, Pearson Education Limited. Statements 3.1 to 3.8 of Topic 3.