Cell theory and prediction

A cell is a membrane-bound unit of living material that can carry out the chemical processes of life. A unicellular organism is a living organism that consists of one cell. A multicellular organism is a living organism composed of many cells, often with different cell types specialized for different jobs.

The key point is not that all cells look alike. They really don't. Cells are the basic structural unit of organisms. A bacterium, a pond protozoan, a plant root and your liver all follow the same cellular principle, even though the details vary enormously.

Cell theory is a scientific theory stating that living organisms are composed of one or more cells and that cells are the fundamental units of structure in organisms. It grew out of repeated microscope observations of many different tissues. Scientists did not inspect every living thing on Earth; they noticed a repeated pattern and generalized from it.

That step, from many specific observations to a broad theory, is inductive reasoning, which is reasoning that builds a general explanation from particular observations. Once cell theory is in place, it allows deductive reasoning, which is reasoning that uses a general theory to make a specific prediction. If scientists discover a completely new organism, the theory lets us predict that it will be made of one or more cells.

Biologists don't throw out a theory just because awkward examples turn up. Some living structures are not typical cells — for example, some extracellular secretions or some unusual multinucleate structures. Cell theory still has power because it explains a huge range of observations and makes useful predictions. A compelling theory does more than label what we already know; it guides what we expect to find next.

Using a light microscope well

A microscope is an optical instrument that uses lenses or electron beams to produce a magnified image of a small object. A light microscope uses visible light and glass lenses to form an image. You should be able to use the eyepiece, objective lenses, stage, condenser or diaphragm, light source, coarse focus and fine focus confidently.

Start on low power. Place the specimen over the light and use the coarse focus to find the image. Then sharpen it with the fine focus. After that, move to a higher-power objective. One small classroom rule protects both slides and lenses: when focusing, move the lens and slide apart, not into each other.

A temporary mount is a microscope slide prepared for short-term viewing by placing a specimen in liquid under a cover slip. The specimen needs to be thin enough for light to pass through, ideally one cell layer thick. Add water or a stain, lower the cover slip at an angle to reduce air bubbles, and touch tissue to the edge of the cover slip to remove excess liquid.

A stain is a coloured chemical that binds selectively to cell components, making structures easier to distinguish. Methylene blue is often used to make nuclei more visible in animal cells; iodine solution can show starch-containing structures in plant material. Air bubbles, dirt and stain crystals are not cell structures. They are artefacts, features introduced during preparation rather than features naturally present in the specimen.

Measuring cells

An eyepiece graticule is a scale fitted in the microscope eyepiece that allows sizes in the field of view to be measured. It is not automatically in micrometres, so it must be calibrated for each objective lens. A stage micrometer is a microscope slide with a known scale used to calibrate the eyepiece graticule.

Measurement with a graticule is a quantitative observation. A quantitative observation is an observation expressed using numbers, usually from counting or measurement. A qualitative observation is an observation expressed as a description rather than a numerical value. “The nucleus stains dark blue” is qualitative; “the cell is $35\,\mu\text{m}$ long” is quantitative.

For images and drawings, use $M = I / A$, where $M$ is magnification (dimensionless), $I$ is image size ($\text{m}$) and $A$ is actual size ($\text{m}$). Rearranging gives $A = I / M$. Make sure the units for $I$ and $A$ match before you calculate. In practice, students often convert mm to $\mu\text{m}$ first because cell sizes are usually most convenient in micrometres.

A scale bar is a labelled line on a drawing or micrograph that represents a stated actual distance in the specimen. To make one, choose the actual length it should represent, multiply by the magnification to find the image length, draw the line, and label it with the actual size. Unlike a written magnification, a scale bar still works if the image is resized.

Recording observations

A photomicrograph is a photograph taken through a microscope. Photographs contain real image data, while a biological drawing can make structure clearer by selecting only relevant edges and features. Use clean single lines with no sketchy shading, and draw only what you can justify from the image. Add annotations with straight ruled label lines; good annotations include the structure name and, where useful, its function.

Resolution matters more than empty magnification

Resolution is the ability of an imaging system to distinguish two close points as separate. Magnification helps only when the resolution is good enough; without it, the image is just a bigger blur. The unaided human eye resolves roughly 0.1 mm, a good light microscope about 0.2 µm, and an electron microscope can resolve much smaller details.

Resolving power improves from the eye to electron microscopy, allowing higher useful magnification.

An electron microscope uses a beam of electrons, rather than visible light, to produce an image. Because electrons have a much shorter wavelength than visible light, electron microscopes can show ultrastructure, the detailed internal structure of cells visible at very high resolution. Mitochondria, ER, ribosomes and membranes therefore appear much clearer in electron micrographs than in light micrographs.

Electron microscopy has real advantages, including high resolution, very high useful magnification and detailed views of cell structure. It also has clear limitations: specimens are dead, preparation can introduce artefacts, images are naturally black and white, and the equipment is expensive and technically demanding. Light microscopy still matters because it can show living cells, movement and natural colour.

Fluorescent staining and immunofluorescence

Fluorescence is emission of light by a substance after it absorbs light of a shorter wavelength. A fluorescent stain binds to a cell component and emits visible light when excited by suitable illumination. Specific structures then stand out brightly against a dark background.

Immunofluorescence is a microscopy technique in which fluorescently labelled antibodies bind to specific antigens in cells. An antibody is a protein produced by immune cells that binds specifically to a particular molecular target. An antigen is a molecule or molecular region that an antibody binds to specifically. With this technique, you can locate a particular protein in a cell, rather than just “see the cell better”.

Freeze fracture

Freeze fracture is an electron microscopy preparation method in which a rapidly frozen specimen is cracked open and a metal replica of the fractured surface is examined. The crack often passes through the middle of phospholipid bilayers, because that is a weak plane in membranes. For this reason, freeze fracture became especially important for understanding membrane structure.

The method gives a surface-like view of internal cell membranes, with a three-dimensional impression created by shadowing the replica with metal. It is not simply a prettier electron micrograph; it reveals membrane faces that ordinary thin sections do not show well.

Cryogenic electron microscopy

Cryogenic electron microscopy is an electron microscopy method in which specimens are rapidly frozen and imaged at very low temperature, preserving structures close to their natural state. It is especially powerful for studying proteins and other molecular complexes.

In cryo-EM, many images of the same type of molecule in different orientations can be combined computationally to reconstruct a three-dimensional structure. One major advantage is that proteins can be caught in different shapes, not only in their most stable form. This helps biologists link molecular structure to function.

The shared toolkit of cells

All typical cells have three essentials: DNA as genetic material, cytoplasm made mainly of water, and a lipid-based plasma membrane. Those details aren’t random. They deal with three basic problems of life: storing instructions, running chemistry, and keeping the cell separate from its surroundings.

A plasma membrane is a lipid-based boundary that encloses a cell and controls exchange with the environment. A cell needs this boundary because its internal chemistry has to stay different from the outside world. Hydrophobic lipid regions make membranes strong barriers to many water-soluble substances, while membrane proteins let selected substances cross. That is one reason all living cells use lipid building blocks: their hydrophobic parts help form compartments.

Cytoplasm is the aqueous material inside the plasma membrane, excluding the nucleus in eukaryotic cells, where many cell reactions occur. Water forms most of it because it dissolves ions and polar molecules very well. Enzymes dissolved or suspended in cytoplasm catalyse metabolic reactions, so cytoplasm is not just “cell jelly”; it works as a busy reaction medium.

Metabolism is the sum of all chemical reactions occurring in a living organism or cell. These reactions release energy, build cell components, break down damaged molecules and maintain internal conditions. Proteins play a central role: enzymes catalyse reactions, membrane proteins control transport, structural proteins give support, motor proteins produce movement, and signalling proteins help cells respond.

DNA is a nucleic acid polymer that stores heritable genetic information in the sequence of its bases. All cells use it because it can be copied and passed to daughter cells. Its form differs between cell types: prokaryotes usually have naked circular DNA in the cytoplasm, while eukaryotes have linear chromosomes associated with histones inside a nucleus, with small circular DNA also present in mitochondria and chloroplasts.

The shared use of DNA, proteins, water and lipid membranes points to common ancestry. Once early cells used these molecular building blocks successfully, descendants inherited and modified them instead of starting again from scratch.

The basic bacterial plan

A prokaryote is a cell or organism whose DNA is not enclosed within a nucleus. In the syllabus, the model is a Gram-positive eubacterium, like the general type shown by Bacillus or Staphylococcus. Prokaryotes vary a lot, so one diagram should not be read as every bacterium on Earth. Still, the basic plan is enough for this topic.

A typical Gram-positive bacterial cell has a cell wall, plasma membrane, cytoplasm, naked DNA in a loop, and $70\text{S}$ ribosomes. A cell wall is a rigid extracellular layer that supports and protects a cell. In Gram-positive eubacteria, it contains a thick layer of peptidoglycan. Peptidoglycan is a strong mesh-like polymer of sugars and short peptides that strengthens bacterial cell walls.

The plasma membrane sits inside the wall and controls exchange. The cytoplasm is not split into organelles by internal membranes. That does not make it chemically simple. It contains enzymes, metabolites, ribosomes and DNA, but it is not compartmentalized like a eukaryotic cell.

A ribosome is a non-membrane-bound particle made of rRNA and protein that synthesizes polypeptides. Prokaryotic ribosomes are $70\text{S}$. The “S” is not a size in metres; it is a Svedberg value for sedimentation behaviour during centrifugation. This matters because prokaryotic $70\text{S}$ ribosomes differ from eukaryotic cytoplasmic $80\text{S}$ ribosomes.

A nucleoid is the region of a prokaryotic cell where the main DNA molecule is located without being enclosed by a membrane. The DNA is usually circular, and naked DNA is DNA not associated with histone proteins. In electron micrographs, the nucleoid often looks paler than the surrounding ribosome-rich cytoplasm.

When identifying prokaryotes in images, look for small size, no nucleus, no membrane-bound organelles, a cell wall, and a nucleoid region. Chains or clusters of small cells are common, but arrangement alone is not enough. Use several features together.

Compartmentalized cells

A eukaryote is a cell or organism whose chromosomes are enclosed in a membrane-bound nucleus. In eukaryotic cells, a plasma membrane surrounds the cytoplasm, and internal membranes divide that cytoplasm into compartments. Different reactions can then happen in separate places, with their own conditions and enzymes.

A nucleus is a double-membrane-bound organelle that contains eukaryotic chromosomes. Its nuclear envelope has pores, which control the movement of molecules such as mRNA out to the cytoplasm. A chromosome is a DNA molecule with associated proteins that carries genetic information. In eukaryotes, chromosomes are linear, and DNA is bound to histones. Histones are basic proteins around which eukaryotic DNA is wound for packaging and regulation.

Eukaryotic cytoplasm contains 80S ribosomes. Some ribosomes float free in the cytosol and make proteins used inside the cell. Others attach to rough endoplasmic reticulum and make proteins for secretion or membranes.

A mitochondrion is a double-membrane-bound organelle that carries out aerobic cell respiration to produce ATP. Its inner membrane is folded, increasing the surface area. A chloroplast is a double-membrane-bound organelle in photosynthetic eukaryotes that carries out photosynthesis. Chloroplasts are not found in all eukaryotic cells, but mitochondria are widespread in eukaryotes.

The endoplasmic reticulum is a membrane system of flattened sacs and tubes involved in synthesis and transport. Rough ER has ribosomes attached; smooth ER does not. The Golgi apparatus is an organelle made of flattened membrane sacs that modifies, sorts and packages cell products in vesicles. A vesicle is a small membrane-bound sac used for transport or storage. A vacuole is a larger membrane-bound sac, often used for storage, digestion or water balance. A lysosome is a membrane-bound vesicle containing digestive enzymes.

The cytoskeleton is a dynamic network of protein fibres that gives cells shape, organizes internal movement and helps cell division. Microtubules are hollow cytoskeletal fibres made of tubulin. Microfilaments are thin cytoskeletal fibres made mainly of actin.

A newly discovered multicellular plant would therefore be expected to have eukaryotic cells: plasma membranes, nuclei with linear DNA-histone chromosomes, cytoplasm with 80S ribosomes, mitochondria, ER, Golgi apparatus, vesicles or vacuoles, cytoskeleton, plus plant features such as cellulose cell walls, chloroplasts in photosynthetic tissues and large sap vacuoles in many mature cells.

One cell, all functions

A unicellular organism is a living organism made of a single cell, and that cell carries out every function needed for survival. In multicellular organisms, tissues share these jobs; in a unicellular organism, one cell does them all.

Homeostasis is the maintenance of internal conditions within tolerable limits. In freshwater unicellular organisms, contractile vacuoles often pump out excess water that enters by osmosis.

Nutrition is the acquisition of materials and energy needed for growth, repair and metabolism. Some unicellular organisms take food particles into food vacuoles; photosynthetic unicellular organisms make organic compounds using light energy.

Movement is a change in position of the whole cell or of materials around it. Cilia and flagella can move cells through water. Cilia are short, numerous surface projections with microtubules that beat to move cells or surrounding fluid. Flagella are longer surface projections with microtubules that beat or undulate to move cells.

Excretion is the removal of metabolic waste products from an organism. In unicellular organisms, small waste molecules often diffuse across the plasma membrane. Don’t mix this up with egestion of undigested food; excretion deals with metabolic waste.

Growth is an increase in size or cell material, or in multicellular organisms an increase in cell number. A unicellular organism grows by producing more cytoplasm, proteins, membranes and genetic material before it divides.

A stimulus is a change in the internal or external environment that an organism can detect. Response to stimuli is the detection of a stimulus followed by an action. A light-sensitive eyespot in a photosynthetic unicell, followed by swimming towards brighter light, is a neat example.

Reproduction is the production of offspring from one or more parent organisms. In many unicellular organisms, this happens by asexual division of one cell into two daughter cells, although some unicellular eukaryotes also have sexual processes.

In the exam, link the structure to the process. A food vacuole shows nutrition and digestion; a contractile vacuole shows homeostasis; cilia or flagella show movement and response; the nucleus and DNA replication support reproduction; the plasma membrane supports exchange and excretion.

Similar eukaryotic plan, different details

Animal, fungal and plant cells are all eukaryotic. They therefore share nuclei, mitochondria, 80S ribosomes, ER, Golgi apparatus and cytoskeleton. The differences that help most are cell walls, vacuoles, plastids, centrioles, cilia and flagella.

A plastid is a double-membrane-bound organelle in plant and algal cells that carries out specialized functions such as photosynthesis or storage. A chloroplast is one type of plastid; an amyloplast stores starch. Animal and fungal cells do not have plastids.

Plant cells have cell walls made mainly of cellulose. Fungal cell walls are made mainly of chitin. Animal cells lack cell walls, so the plasma membrane, cytoskeleton and surrounding extracellular material maintain their surface shape rather than a rigid wall.

A sap vacuole is a large permanent vacuole in many plant cells that stores cell sap and helps maintain turgor pressure. Fungal cells may also have large vacuoles for storage and internal digestion. In animal cells, vacuoles or vesicles are usually small and temporary, rather than one large permanent sap vacuole.

A centriole is a cylindrical structure made from microtubules that helps organize microtubule assembly in many animal cells. Animal cells commonly have centrioles; typical plant and fungal cells do not, except in lineages or stages with swimming gametes. Cilia and flagella occur in many animal cells and in some motile gametes, but typical plant and fungal body cells lack them.

Key structural differences between animal, fungal and plant eukaryotic cells.

When you identify cells, use a combination of features. A cellulose wall plus chloroplasts strongly suggests plant; a chitin wall without chloroplasts suggests fungus; no wall plus centrioles or cilia suggests animal. One feature alone can mislead, especially because not every plant cell has visible chloroplasts.

When “one cell, one nucleus” breaks down

Most eukaryotic cells have one nucleus. Biology, though, has some useful exceptions. These unusual structures don't weaken cell theory; they show how far cells can be adapted for particular functions.

A red blood cell in mammals is specialized for oxygen transport and has no nucleus when mature. Without the nucleus, there is more internal space for haemoglobin, and the cell can become more flexible. The cost is clear: it cannot repair itself well or divide.

A phloem sieve tube element is a plant transport cell that conducts sugar-rich sap and lacks a nucleus at maturity. It still keeps its plasma membrane, since phloem transport depends on living membrane function, but it depends on a neighbouring companion cell for support. With fewer internal obstructions, sap can move through the sieve plates.

A skeletal muscle fibre is a long contractile structure made when many precursor cells fuse, so it contains many nuclei. A syncytium is a multinucleate structure formed by cell fusion. Muscle fibres are large and contain a high volume of cytoplasm packed with contractile proteins, so they need many nuclei to maintain it.

An aseptate fungal hypha is a fungal filament with no cross-walls between nuclear regions. A septum is a cross-wall that divides fungal hyphae into cell-like compartments. A coenocyte is a multinucleate mass of cytoplasm produced by repeated nuclear division without cell division. In aseptate hyphae, many nuclei share one continuous cytoplasm.

For the syllabus, use number of nuclei as the comparison: red blood cells and sieve tube elements have no nucleus; typical cells have one; skeletal muscle fibres and aseptate fungal hyphae have many. That's the simple thread linking these examples.

Identifying whole cells in micrographs

A micrograph is an image produced using a microscope. In light micrographs, start by classifying the cell type from its size, outline and the main structures you can see. Prokaryotes are usually small, often under $5\,\mu\text{m}$, and have no nucleus or membrane-bound organelles. Plant cells are usually larger, often with straight-edged walls; chloroplasts or a large vacuole may be visible. Animal cells are usually larger than prokaryotes, lack cell walls, and often have rounded or irregular outlines.

In electron micrographs, ultrastructure gives more clues. Prokaryotes show a nucleoid region, cell wall, plasma membrane, cytoplasm and ribosomes, but no nucleus, mitochondria, ER, Golgi apparatus or chloroplasts. Plant and animal cells both show eukaryotic organelles; plant cells may also show a cell wall, chloroplasts and a sap vacuole.

Identifying structures in electron micrographs

The prokaryotic cell wall is the rigid outer layer surrounding many bacterial cells. The nucleoid region looks like a less densely stained region containing naked DNA. Prokaryotic ribosomes show up as tiny dark granules in the cytoplasm.

The nucleus is usually the largest organelle, enclosed by a double nuclear envelope with pores. Chromosomes may appear as diffuse chromatin or, during division, as condensed stained bodies. Chromatin is DNA associated with proteins in a less condensed state inside the nucleus.

A mitochondrion can be recognized by its double membrane and internal folds called cristae. A chloroplast has a double membrane and internal thylakoid membranes, often arranged in stacks; starch grains may also be visible.

A sap vacuole appears as a large clear membrane-bound compartment in many plant cells. The Golgi apparatus looks like a stack of flattened, curved membrane sacs, usually with small vesicles nearby. Rough endoplasmic reticulum appears as flattened membranes with ribosomes attached, whereas smooth endoplasmic reticulum appears as tubular membranes without ribosomes.

A ribosome appears as a tiny dense granule and is not membrane-bound. The cell wall in plant and fungal cells lies outside the plasma membrane and looks thicker and more rigid. The plasma membrane is a thin boundary line around the cytoplasm, often easier to infer than to see directly.

Microvilli are short plasma membrane projections that increase surface area for absorption. They are common on some animal epithelial cells and appear as many small parallel projections on the cell surface.

A useful link is the variety of genetic material. Prokaryotes usually show circular naked DNA in a nucleoid, eukaryotic nuclei contain linear DNA bound to histones as chromosomes, and mitochondria and chloroplasts contain their own small circular DNA. Same molecular role, different cellular form.

Turning an electron micrograph into a useful biological drawing

An annotation is a label with an explanatory note, often including a function. For this content statement, naming the structure isn’t enough: the annotation needs to link structure to function.

When you draw from an electron micrograph, focus on what matters biologically rather than every speck of stain. Use clear outlines. Keep the proportions sensible. Avoid shading unless it shows a real boundary, and use ruled label lines that do not cross. If the micrograph shows an artefact, leave it out unless the task asks you to identify it.

You should be able to draw and annotate these organelles when they are shown: nucleus, mitochondria, chloroplasts, sap vacuole, Golgi apparatus, rough ER, smooth ER and chromosomes. You should also be able to draw and annotate cell wall, plasma membrane, secretory vesicles and microvilli.

A secretory vesicle is a membrane-bound sac that carries substances to the plasma membrane for release from the cell. In an annotation, a vesicle near the Golgi could be described as transporting processed protein for secretion. Microvilli should be annotated as increasing surface area for absorption. A mitochondrion should be annotated as carrying out aerobic respiration to supply ATP. Rough ER should be annotated as protein synthesis and transport, especially for secreted or membrane proteins.

Good annotations are brief but functional: “nuclear envelope with pores — controls movement of mRNA and proteins between nucleus and cytoplasm” is much better than simply “nucleus”. The drawing is your interpretation of the micrograph; the annotations show that you understand the biology behind the shapes.

Endosymbiosis and eukaryotic origins

Symbiosis is a close, long-term association between organisms of different types. Endosymbiosis is a symbiotic relationship where one organism lives inside another organism, or inside another cell. The theory of endosymbiosis says that mitochondria, and later chloroplasts in some lineages, evolved from free-living prokaryotes that became permanent internal partners of early eukaryotic cells.

Evidence suggests all living eukaryotes share a common unicellular ancestor that had a nucleus and reproduced sexually. Mitochondria then evolved by endosymbiosis in this lineage. In photosynthetic eukaryotic lineages, chloroplasts evolved later, when a host cell retained a photosynthetic prokaryote inside it.

Several independent observations make the evidence strong. Mitochondria and chloroplasts contain 70S ribosomes, like prokaryotes. They also contain naked circular DNA, unlike nuclear eukaryotic chromosomes. They replicate by division of pre-existing mitochondria or chloroplasts. These observations fit exactly what the theory predicts if these organelles descended from bacteria-like endosymbionts.

A compelling theory explains observations and supports predictions. Endosymbiotic theory explains why mitochondria and chloroplasts have double membranes, why they have their own DNA, why their ribosomes resemble prokaryotic ribosomes, and why they divide independently of the nucleus. It also predicts that molecular comparisons should link mitochondria and chloroplasts more closely to bacterial lineages than to the eukaryotic nucleus — and that prediction is supported.

Natural selection makes the scenario plausible. A host cell that kept an aerobic endosymbiont gained more efficient ATP production; the endosymbiont gained nutrients and protection. Later, a host that retained a photosynthetic endosymbiont gained access to sugars made from light energy. Partnerships that improved survival and reproduction would become more common over generations.

Same genome, different cell behaviour

Cell differentiation is the process by which cells develop specialized structures and functions by following different patterns of gene expression. In a multicellular organism, most cells carry the same genetic information. They just don’t use all genes to the same extent.

Gene expression is the process by which information in a gene is used to produce a functional product, usually RNA or protein. A red blood cell precursor strongly expresses genes for haemoglobin; a pancreatic secretory cell strongly expresses genes for digestive enzymes. Usually, the difference is not that the cells have different genes. It’s that different genes are active.

Housekeeping genes are genes expressed in many or all cell types because they are needed for basic cell survival. Genes involved in core respiration, transcription, translation and membrane maintenance are examples of activity that every living cell needs. Specialized genes are expressed only in particular cells or at particular times.

The environment can trigger differentiation. Here, “environment” can mean signals from neighbouring cells, gradients of chemical signals in an embryo, hormones, nutrients or physical conditions. These signals change patterns of gene expression. As a result, cells make different proteins, and their structure and function change. That is how specialized tissues develop from cells that were initially less specialized.