Cell Structure¶

Part of Module 2: Foundations in biology.

Cell structure is the foundation for almost every later topic. It establishes two habits early: looking carefully at real biological material through the lens of microscopy, and linking visible structure directly to function. The topic moves from microscopy and scale, through organelle biology and cell types, and out to a systematic comparison of prokaryotes and eukaryotes.

Learning Objectives¶

Magnification and Resolution¶

Two terms define the quality of any microscopic image, and they must never be confused.

Magnification is how many times larger the image is than the real object. The equation is:

magnification = image size ÷ object size

All lengths must be in the same unit before performing the calculation. This almost always requires a unit conversion: to convert mm into µm, multiply by 1,000; to convert µm back to mm, divide by 1,000.

Worked example — calculating magnification: A plant cell in a micrograph measures 40 mm in width. The real width of the cell is 20 µm. What is the magnification?

1. Convert image size into µm: 40 mm × 1,000 = 40,000 µm
2. Apply the formula: magnification = 40,000 ÷ 20 = ×2,000

Worked example — calculating image size: A sperm cell is 5 µm long. How long will it appear in mm under a microscope with a magnification of ×1,500?

1. Rearrange the formula: image size = magnification × object size
2. Calculate: 1,500 × 5 = 7,500 µm
3. Convert to mm: 7,500 ÷ 1,000 = 7.5 mm

Resolution is the ability to distinguish two close points as separate. A large blurred image can still have very poor resolution. Electron microscopes have shorter-wavelength electrons compared to light waves, giving them far better resolution than light microscopes. This is why ultrastructure — the fine internal detail of organelles — can only be seen with an electron microscope.

Calibrating a Microscope: The Eyepiece Graticule¶

When measuring cell dimensions under a light microscope, an eyepiece graticule is used. This is a small numbered scale (typically 0–100) placed inside the eyepiece. Because the graticule divisions represent different real-world distances at different objective lens magnifications, the graticule must be calibrated for each objective lens used.

Calibration is performed using a stage micrometer — a glass slide engraved with a scale measured in µm.

Calibration procedure: 1. Fix the stage micrometer onto the stage. 2. Look through the eyepiece and align the micrometer scale alongside the graticule. 3. Count the number of graticule divisions that span one micrometer division. 4. Apply the formula:

graticule division size = size of one micrometer division ÷ number of graticule divisions

Worked example: Each division on the stage micrometer represents 10 µm. When aligned, 40 graticule divisions span one micrometer division.

graticule division size = 10 ÷ 40 = 0.25 µm per graticule division

Once calibrated at a given magnification, any specimen dimension can be estimated by counting graticule divisions and multiplying by this value.

Types of Microscope¶

Light (Optical) Microscopes¶

Light microscopes form images by passing visible light through the specimen. They are the main classroom tool because specimens can be alive, sample preparation is simple, and images are produced in colour.

Transmission Electron Microscopes (TEM)¶

TEMs use electromagnets to transmit a beam of electrons through an ultra-thin specimen. Denser regions absorb more electrons and appear darker. TEMs produce high-resolution 2D images that reveal the internal ultrastructure of organelles — for example, the internal thylakoid membranes of a chloroplast, or the cristae of a mitochondrion.

The specimen must be thin enough for electrons to pass through, and it must be viewed in a vacuum, so only non-living material can be observed.

Scanning Electron Microscopes (SEM)¶

SEMs scan a beam of electrons across the surface of the specimen and detect reflected electrons to build a three-dimensional image of surface features. Thicker specimens can be used compared to TEM.

Laser Scanning Confocal Microscopes¶

Laser scanning confocal microscopy is a form of fluorescence microscopy. A focused laser beam scans across a specimen that has been labelled with a fluorescent dye. The dyed components emit light, which is passed through a pinhole that blocks out-of-focus light before reaching a detector connected to a computer. The pinhole is the key innovation: it eliminates blurring from tissue at different depths, producing much clearer images than conventional light microscopy.

The resulting images can be converted into three-dimensional reconstructions. Crucially, this type of microscope can be used to observe living specimens and to image at different depths within a specimen. Its resolution is better than a conventional light microscope but lower than electron microscopes.

Comparing all four microscope types:

All electron microscopes produce images in black and white (though computers can add false colour). Both TEM and SEM require complex specimen preparation and are more likely to introduce artefacts — visible features that are not genuinely part of the specimen, such as air bubbles or preparation debris.

Preparing Samples for Light Microscopy¶

Wet Mounts¶

Most biological specimens are prepared as wet (temporary) mounts:

1. Place a small drop of water onto the centre of a glass slide using a pipette.
2. Use forceps to place a thin section of the specimen onto the water. The section must be thin enough to allow light to pass through.
3. Add a few drops of stain (for example, iodine in potassium iodide) to increase contrast and reveal cell components.
4. Slowly lower a cover slip onto the specimen to avoid trapping air bubbles.

Staining is essential for most specimens because many cell structures are transparent and impossible to distinguish without contrast enhancement. Differential staining (using more than one stain) can be used to distinguish between different cell types or organelle types simultaneously.

Other Slide Types¶

• Dry mounts: the specimen is placed directly onto the slide and covered with a cover slip, without water. Used for dry or powdered material.
• Squash slides: a wet mount is prepared, then the cover slip is gently pressed to flatten and separate the cells.
• Smear slides: the edge of a second slide is used to smear the sample across the slide surface, producing a thin, even coating. Commonly used for blood films.

Using the Microscope¶

1. Clip the prepared slide onto the stage.
2. Select the lowest-power objective lens.
3. Use the coarse focus to bring the stage up close to the objective lens.
4. Looking down the eyepiece, use coarse focus to move the stage down until the image comes roughly into focus.
5. Use the fine focus to sharpen the image.
6. If a higher magnification is needed, switch to a higher-power objective lens and refocus.

Biological Drawings¶

Biological drawings are used to record observations when viewing specimens. They must adhere to specific conventions.

A biological drawing should: - Have a title - State the magnification or include a scale bar - Be drawn with a sharp pencil - Use smooth, continuous lines (no sketchy strokes) - Include clear labels - Accurately represent the relative sizes of observable structures

A biological drawing should NOT: - Include shading or colouring - Use arrowheads on label lines - Have label lines that overlap each other

Animal Cell Organelles¶

Animal cells are eukaryotic — they have a nucleus enclosed by a membrane and a range of membrane-bound organelles in the cytoplasm.

Nucleus¶

The nucleus is the largest organelle in most animal cells. Its key structural features are: - Chromosomes containing the cell's genetic information as DNA - A nucleolus that synthesises ribosomal RNA (rRNA) for ribosome assembly - A nuclear envelope (double membrane) perforated by nuclear pores that allow exchange of substances between the nucleus and cytoplasm

The nucleus directs cell activity by providing DNA templates for protein synthesis. Signals and molecules pass through the nuclear pores in both directions.

Cell-Surface Membrane¶

Also called the plasma membrane, this is a partially permeable barrier made mainly of lipids and protein. It controls the movement of substances into and out of the cell and carries receptor proteins for cell signalling. The detailed molecular structure (the fluid-mosaic model) is developed in 2.1.5 Biological membranes.

Mitochondria¶

Mitochondria are found in large numbers in cells with high energy demands. Their structure is closely matched to their function: - A double membrane: the inner membrane is folded into projections called cristae, which greatly increase surface area for the reactions of aerobic respiration - A fluid matrix that is rich in enzymes and contains the mitochondrion's own DNA (mtDNA) and ribosomes

The presence of their own DNA and ribosomes is important: mitochondria replicate semi-autonomously within the cell and their ribosomes are 70S (the same size as prokaryotic ribosomes), supporting the endosymbiotic theory of their evolutionary origin.

Ribosomes¶

Ribosomes are the sites of protein synthesis. They are not membrane-bound. In eukaryotic cells, ribosomes are 80S, composed of a large and a small subunit, and made of proteins and ribosomal RNA (rRNA). They are found either free in the cytoplasm or attached to rough ER.

Rough Endoplasmic Reticulum (RER)¶

The RER is a network of membrane-enclosed cisternae (flattened, fluid-filled sacs) studded with ribosomes. Proteins are synthesised on those ribosomes and enter the cisternal lumen for folding, modification, and packaging into transport vesicles destined for the Golgi apparatus.

Smooth Endoplasmic Reticulum (SER)¶

The SER has the same basic membrane network structure as the RER but lacks ribosomes. It is the site of synthesis, storage, and transport of lipids and carbohydrates, including cholesterol and steroid hormones.

Golgi Apparatus¶

The Golgi apparatus (or Golgi body) consists of stacked, flattened, membrane-bound cisternae flanked by vesicles. Its functions are to: - Process and package proteins and lipids received from the ER - Store and transport these molecules in vesicles that bud off from the cisternae - Synthesise lysosomes as specialised vesicles

Lysosomes¶

Lysosomes are spherical, membrane-bound vesicles containing hydrolytic enzymes. The membrane keeps these enzymes isolated from the cytoplasm. Lysosomes digest pathogens engulfed by phagocytosis and break down waste material including old organelles and cellular debris.

Cytoskeleton¶

The cytoskeleton is a dynamic protein framework extending throughout the cytoplasm. It consists of three main components:

• Microfilaments: made of the protein actin. They drive cell movement, cell crawling, and muscle contraction.
• Microtubules: made of the protein tubulin. They form a scaffold throughout the cell, serve as tracks for intracellular transport of vesicles and organelles, and form the mitotic spindle during cell division.
• Intermediate filaments: maintain the position of organelles within the cell and provide mechanical strength to tissues such as skin and hair.

Plant Cell Organelles¶

Plant cells share all the organelles described for animal cells and additionally contain:

Cell Wall¶

The plant cell wall surrounds the cell outside the plasma membrane and provides rigidity. It is made of cellulose microfibrils arranged in layers. Key features: - It can withstand high osmotic pressure, preventing the cell from bursting when turgid - It contains channels called plasmodesmata (singular: plasmodesma) that link neighbouring cells and allow exchange of substances between them

Chloroplasts¶

Chloroplasts are the organelles of photosynthesis, found in the green parts of the plant (leaves, stems). Their structure: - A double membrane surrounding the whole organelle - Internal fluid called the stroma, where certain reactions of photosynthesis occur - Membrane-bound fluid-filled sacs called thylakoids, stacked into structures called grana (singular: granum), where light-dependent reactions occur - Their own DNA and ribosomes (70S), again supporting endosymbiotic origin

Permanent Vacuole¶

Plant cells have a large, central, permanent vacuole containing cell sap (a solution of salts, sugars, and other dissolved substances). The vacuole is surrounded by a selectively permeable membrane called the tonoplast. The vacuole maintains turgor pressure within the cell: as water enters by osmosis, the contents press outward against the cell wall, keeping the cell firm and preventing wilting.

Algal and Fungal Cells¶

Algal cells contain the same organelles as plant cells, including chloroplasts (though the chloroplast shape may differ from plant chloroplasts). They may be unicellular or multicellular.

Fungal cells contain most of the organelles found in plant cells but do not contain chloroplasts (fungi are heterotrophic). Their cell walls are made of chitin rather than cellulose.

Prokaryotic Cells¶

Prokaryotes are single-celled organisms — bacteria are the main example. They are much smaller than eukaryotic cells and lack a nucleus and all membrane-bound organelles.

Key Structural Features of Prokaryotes¶

• Cell wall: present in all prokaryotes, made of murein (peptidoglycan) — a different polymer from the cellulose of plant walls or the chitin of fungal walls.
• Circular DNA: the genetic material is a single large circular strand of DNA located in the nucleoid region (not enclosed in a membrane).
• Plasmids: small, additional circular loops of DNA carrying genes such as antibiotic resistance genes, separate from the main chromosome.
• 70S ribosomes: smaller than the 80S ribosomes of eukaryotes.
• Capsule (present in some prokaryotes): an outer layer of polysaccharides surrounding the cell wall. It protects the cell from attack by antibiotics or white blood cells.
• Flagellum (plural: flagella): a long, rotating, hair-like structure attached to the cell membrane that propels the cell through its environment.
• Pili (singular: pilus): short, hair-like projections used to attach the cell to surfaces or to other cells (important in conjugation and biofilm formation).

Protein Secretion Pathway¶

A key integrating concept is how organelles work as a coordinated system rather than isolated structures. A protein destined for secretion is synthesised and exported in a defined sequence:

1. The gene in the nucleus is transcribed to produce mRNA, which exits through nuclear pores.
2. The mRNA attaches to ribosomes on the rough ER, where translation produces the polypeptide chain.
3. The protein is folded and initially modified inside the ER cisternae.
4. The protein is packaged into a transport vesicle that buds off from the ER.
5. The transport vesicle fuses with the Golgi apparatus, delivering the protein.
6. The Golgi modifies and repackages the protein into secretory vesicles.
7. The secretory vesicle fuses with the cell-surface membrane and releases the protein outside the cell by exocytosis.

This pathway shows that organelles are not separate facts but components of a functional system. The full molecular story of transcription and translation is developed in 2.1.3 Nucleotides and nucleic acids.

Prokaryotes vs Eukaryotes: Systematic Comparison¶

Shared features (present in both cell types): cell-surface membrane, cytoplasm, ribosomes, and DNA.

Common Confusions¶

• Magnification is not the same as resolution. A large blurred image has high magnification but poor resolution. Resolution depends on wavelength: light has longer wavelengths than electrons, so light microscopes always have lower resolution than electron microscopes regardless of magnification.
• Prokaryotic cells do have DNA and ribosomes. The distinction is that they lack membrane-bound organelles. Students who state "prokaryotes have no organelles" are wrong — they have ribosomes.
• All electron microscopes produce dead specimens and require vacuum conditions. Confocal microscopes are the key exception that allows imaging of living cells at high clarity.
• The Golgi apparatus both modifies and synthesises. It is not simply a packaging station: it also produces new molecular modifications and generates lysosomes.
• Chloroplasts and mitochondria have 70S ribosomes, not 80S, because of their prokaryotic evolutionary origin.

Practical Skills¶

Practical work (PAG1) links directly to this topic. Key skills include: - Preparing wet mount, dry mount, squash, and smear slides - Applying stains appropriately - Using a light microscope at increasing magnifications - Producing accurate biological drawings - Calibrating an eyepiece graticule using a stage micrometer - Performing magnification and scale calculations

The mathematics is scale-based: magnification formula, unit conversion between mm and µm, and graticule calibration. Exact resolution figures should be known for light microscopes (0.2 µm), TEM (0.5 nm), and SEM (5 nm).

Key Terms¶

• Magnification: how many times larger the image is than the real object; calculated as image size divided by object size.
• Resolution: the ability to distinguish two close points as separate; depends on the wavelength of radiation used.
• Ultrastructure: the fine internal detail of cell structure visible with an electron microscope.
• Eyepiece graticule: a numbered scale in the eyepiece used to measure specimen dimensions; must be calibrated against a stage micrometer.
• Stage micrometer: a glass slide engraved with a scale in µm, used to calibrate the eyepiece graticule.
• Artefact: a visible feature in a microscope image that is not genuinely part of the specimen, introduced during preparation.
• Eukaryotic cell: a cell with a nucleus and membrane-bound organelles (animals, plants, fungi, protists).
• Prokaryotic cell: a cell without a nucleus or membrane-bound organelles; DNA is circular and found in the nucleoid region.
• Nuclear envelope: the double membrane surrounding the eukaryotic nucleus, perforated by nuclear pores.
• Nucleolus: the region within the nucleus where ribosomal RNA is synthesised.
• Cristae: the folds of the inner mitochondrial membrane that increase the surface area available for aerobic respiration.
• Cisternae: flattened, fluid-filled membrane sacs found in the RER, SER, and Golgi apparatus.
• Plasmodesmata: channels through plant cell walls that connect neighbouring cells.
• Tonoplast: the selectively permeable membrane surrounding the plant cell vacuole.
• Thylakoids: membrane-bound sacs within chloroplasts, stacked into grana, where light-dependent reactions of photosynthesis occur.
• Murein (peptidoglycan): the polymer making up prokaryotic cell walls.
• Plasmid: a small, circular loop of DNA in prokaryotes, carrying additional genes separate from the main chromosome.
• Capsule: polysaccharide outer layer found in some prokaryotes, protecting against attack by white blood cells and antibiotics.

Connected Pages¶

• 2.1.2 Biological molecules
• 2.1.3 Nucleotides and nucleic acids
• 2.1.5 Biological membranes