Cell Structure, Tissues & Viruses — A-Level Biology Revision Notes

Microscopy — Light vs Electron Microscopes

All our knowledge of cell ultrastructure depends on microscopes. There are two main types used in biology, and understanding the differences between them is essential for interpreting micrographs and understanding why certain organelles can or cannot be seen.

Resolution vs Magnification

The critical difference is resolution, not magnification. Cell organelles lie very close together inside cells. The wavelength of light is too long to pass between smaller organelles, so the light microscope cannot resolve (separate) them — the cell interior appears largely empty apart from the nucleus and chloroplasts, which are large enough to resolve. Electrons have a much shorter wavelength, allowing them to pass between smaller organelles, producing images with very high resolution where fine detail (mitochondria, ribosomes, ER) becomes visible.

Magnification Calculations & Units

Units of Length in Biology

The Magnification Equation

The central equation for all microscopy calculations is: Magnification = Image size ÷ Actual size. This can be rearranged: Actual size = Image size ÷ Magnification, and Image size = Actual size × Magnification. Both measurements must be in the same units before you calculate — always convert to the smaller unit (typically µm or nm).

Scale Bars on Micrographs

Micrographs often include a scale bar rather than quoting magnification directly. The number on the scale bar represents the actual length. You measure the drawn length of the scale bar in cm or mm, then use the magnification equation: magnification = drawn length of scale bar ÷ actual length stated on scale bar. Once you know the magnification, you can calculate the actual size of any structure in the micrograph.

Calibrating the Light Microscope

To make real measurements under the light microscope, you need an eyepiece graticule (a scale inside the eyepiece, measured in arbitrary eyepiece units, epu) and a stage micrometer (a slide with a known real scale, typically 10 mm divided into 100 divisions). By aligning both scales and comparing readings, you calculate the calibration value — the real size of one eyepiece unit. This must be calculated separately for each objective magnification (×40, ×100, ×400).

The Cell Theory

The cell theory is a foundational scientific theory that has been developed and refined over centuries as microscope technology improved. Its key principles are:

All living things are composed of cells and cell products. New cells are formed by the division of pre-existing cells — they do not arise spontaneously. The cell contains inherited information (DNA) that provides instructions for growth, functioning, and development. The cell is the functional unit of life — all the chemical reactions of life (metabolism) take place within cells.

The Nucleus, DNA & Ribosomes

The Nucleus (~10 µm diameter)

The nucleus is the largest organelle and is present in all plant and animal cells except mature red blood cells. There is typically one nucleus per cell. The nucleus is one of three organelles with a double membrane — this is called the nuclear envelope. The nuclear envelope contains many nuclear pores which allow the passage of substances such as mRNA and ribosomal subunits out of the nucleus into the cytoplasm.

Inside the nucleus, DNA is coiled around protein spheres called histones to form chromatin (which appears as dark-staining material under the electron microscope). Also visible is the nucleolus (1–2 µm diameter) — a dense, darkly staining round structure that is the site of ribosomal RNA (rRNA) synthesis. Because the nucleus contains the cell’s DNA, it controls all cellular activities including protein synthesis and cell division. DNA contains the genetic code — the instructions for making all the cell’s proteins.

Ribosomes (~20 nm)

Ribosomes are the site of protein synthesis, where amino acids are joined together by peptide bonds. Each ribosome consists of a large subunit and a small subunit, both made of rRNA and protein. There are two types: 80S ribosomes (larger, found in eukaryotic cells — on the RER and free in the cytoplasm) and 70S ribosomes (smaller, found in prokaryotic cells and also inside mitochondria and chloroplasts).

Endoplasmic Reticulum & Golgi Body

Rough Endoplasmic Reticulum (RER)

The RER is an extensive network of flattened, interconnected cavities called cisternae that span throughout the cytoplasm and around the nucleus, forming a regular parallel arrangement. It is an extension of the outer nuclear envelope. The surface of the cisternae is studded with 80S ribosomes — this gives it the “rough” appearance under the electron microscope. The ribosome component synthesises proteins, while the ER component transports proteins through the cell. The RER also forms transport vesicles that bud off and carry proteins to the Golgi body.

Smooth Endoplasmic Reticulum (SER)

The SER forms from the RER but has a tubular structure with no ribosomes on its surface, forming an irregular arrangement in the cytoplasm. Its primary function is the synthesis of lipids (including phospholipids) and steroids (e.g. testosterone, oestrogen). Other functions include storage of calcium ions (in muscle cells, where the SER is called the sarcoplasmic reticulum) and detoxification of drugs and poisons (in liver cells). The SER is found in high abundance in liver cells, muscle cells, and the ovaries and testes.

Golgi Body (Golgi Apparatus)

The Golgi body consists of flattened sacs called cisternae that are not interconnected (unlike the ER). Vesicles from the RER arrive and fuse at one end, while secretory vesicles bud off at the other end and transport proteins to the cell membrane for release by exocytosis. The Golgi body functions to: modify proteins (by adding carbohydrate chains to form glycoproteins), package proteins into vesicles for secretion, produce lysosomes, and transport and sort lipids.

Lysosomes (0.1–1.0 µm)

Lysosomes are spherical vesicles produced by the Golgi body. They contain approximately 50 different hydrolytic enzymes. Their functions include: digestion of material taken into the cell from outside (e.g. bacteria engulfed by phagocytosis — the food vacuole fuses with a lysosome for digestion), and digestion of worn-out organelles and biological molecules (autophagy).

The Protein Secretion Pathway

This pathway describes the journey of a protein from its synthesis to its export from the cell. It links together several organelles in sequence and is a commonly examined topic across all boards:

Mitochondria (~6 µm)

Mitochondria are the site of aerobic respiration, where glucose is converted into molecules of ATP (adenosine triphosphate). Each mitochondrion has the following structural features:

Double membrane — an outer membrane and a highly folded inner membrane. The folds of the inner membrane are called cristae, which increase the surface area for the reactions of aerobic respiration. On the cristae are stalked particles (ATP synthase enzymes). Between the outer and inner membranes is the intermembrane space. The interior is filled with a fluid called the matrix, which contains enzymes for the Krebs cycle. Mitochondria also contain their own 70S ribosomes and circular DNA, which allows them to self-replicate and produce some of their own proteins.

Why Mitochondria Appear Different in Micrographs

In electron micrographs, mitochondria in the same cell can appear as sausage-shaped or circular. This is because the organelles lie at different angles within the cell, and the plane of cut (the angle at which the specimen is sliced) determines the cross-sectional shape. A longitudinal cut through a sausage-shaped mitochondrion produces an elongated profile; a transverse cut through the same organelle produces a circular profile.

Chloroplasts (~10 µm)

Chloroplasts are the organelles in which photosynthesis occurs. They contain chlorophyll, the organic pigment that absorbs light energy. Chloroplasts share several features with mitochondria but have a distinct internal membrane system:

Double membrane (outer and inner). A fluid stroma (equivalent to the mitochondrial matrix) containing enzymes for the Calvin cycle. Internal membranous structures called thylakoids — flattened, disc-like sacs where the light-dependent reactions occur. Thylakoids stack on top of each other to form grana (singular: granum). Grana are linked together by inter-granal lamellae. Like mitochondria, chloroplasts contain their own 70S ribosomes, circular DNA, and can self-replicate. Starch grains and lipid globules may also be visible.

The Endosymbiont Theory

The endosymbiont theory proposes that mitochondria and chloroplasts were once free-living prokaryotic organisms that were engulfed by a larger ancestral eukaryotic cell. Rather than being digested, they formed a mutually beneficial (symbiotic) relationship — the prokaryote gained protection and nutrients, while the host cell gained the ability to carry out aerobic respiration or photosynthesis.

The evidence supporting this theory comes from the striking similarities between these organelles and prokaryotic cells: both mitochondria and chloroplasts have a double membrane (the inner membrane from the original prokaryote, the outer from the host’s engulfing membrane), their own circular DNA (like bacterial chromosomes, not linear like eukaryotic DNA), 70S ribosomes (the same size as bacterial ribosomes, not 80S), and the ability to self-replicate by binary fission (as bacteria do). They are also approximately the same size as bacteria.

Plant-Specific Structures

Cell Membrane (~7–9 nm thick)

The cell membrane has a bilayer structure made of phospholipids with various proteins positioned within and on its surface. Its function is to regulate the entry and exit of substances. This structure is covered in detail in the Cell Membrane resources page.

Cellulose Cell Wall

Plant cells have a rigid cell wall made of cellulose that lies outside the cell membrane. Its functions are: providing mechanical strength and support to cells, being freely permeable to water and dissolved substances (it is not selectively permeable like the cell membrane), and allowing cells to become turgid when water enters by osmosis (the inelastic wall prevents bursting and generates pressure potential).

Vacuole

Plant cells have a large permanent vacuole surrounded by a membrane called the tonoplast. The vacuole contains cell sap — a solution of sugars and amino acids dissolved in water. Its functions include: water enters by osmosis to make the cell turgid, acting as food storage, accumulation of waste products, and in some plants containing coloured pigments (e.g. the red pigment in beetroot cells used in the membrane permeability practical).

Plasmodesmata

Plasmodesmata are narrow pores in the cell wall that connect neighbouring plant cells. They create cytoplasmic channels through which water and dissolved substances can move directly between adjacent cells — this is the symplast pathway of water movement through plant tissue.

Centrioles & Cilia

Centrioles

Centrioles are two short bundles of microtubules arranged in triplets, positioned at right angles to each other near the nucleus. Their function is to form the spindle fibres during cell division (mitosis and meiosis). Centrioles are found in animal cells but are absent in most higher plant cells (plants use a different mechanism to form spindle fibres).

Cilia

Cilia are hair-like structures that project from the surface of certain cells. In the trachea of the lungs, the ciliated epithelial cells are covered in mucus that traps bacteria and other particles. The cilia then waft the mucus upward and out of the lungs, preventing infection. In the fallopian tubes, cilia waft the egg cell towards the uterus.

Prokaryotic Cells

Prokaryotic cells are bacteria. They are smaller (0.1–10 µm) and simpler than eukaryotic cells — they have no nucleus and no membrane-bound organelles.

Tissues, Organs & Organ Systems

Epithelial Tissues

Muscle Tissues

Connective Tissues

Cartilage has a matrix containing chondrin with embedded chondrocytes and fine collagen fibres — hard but flexible. Found at bone ends, ear, nose, and respiratory system. Bone has a matrix of collagen with inorganic calcium and phosphorus. Bone cells (osteocytes) are arranged in concentric circles called lamellae forming Haversian systems, each with a central canal containing blood vessels and nerves.

Viruses

Viruses are extremely small structures (20–300 nm) that are not cells — they have no organelles, no metabolism, and cannot reproduce independently. They can only survive and replicate by infecting host cells and hijacking their biochemical machinery. For this reason, viruses are described as obligate intracellular parasites. Viruses that infect bacteria are called bacteriophages.

Structure of a Typical Animal Virus

A virus consists of a protein coat (capsid) with embedded surface antigens (which make the virus pathogenic and allow it to bind to host cells). Inside the capsid is the nucleic acid — either DNA or RNA, but never both. Viruses containing RNA are called retroviruses (e.g. HIV).

Viral Replication — The Lytic Cycle

Where Cell Structure Appears on Your Specification

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