Chapter 1.3: Cells (CCEA AS Biology Unit 1)
Welcome to your study notes for Cells! Cells are the fundamental building blocks of all living organisms. In this chapter, we explore the microscopic world: how we view cells, what makes up eukaryotic and prokaryotic cells, the architecture of viruses, and how scientists isolate individual organelles. Don't worry if cell ultrastructure feels overwhelming at first—we will break down every organelle and technique step-by-step.
Exam Note: This topic is examined in Unit AS 1: Molecules and Cells (Paper Code: SBY11). The terminology you learn here is essential for both the structured questions in Section A and the 15-mark extended response essay in Section B where your Quality of Written Communication (QWC) is assessed.
---1. Microscopy, Magnification, and Calibration
Magnification vs. Resolution
It is very common to confuse magnification with resolution. Here is the distinction:
• Magnification: The number of times larger an image is compared to the actual size of the specimen.
• Resolution: The minimum distance between two separate points at which they can still be distinguished as two distinct entities. High resolution means greater detail and clarity.
Examiner Tip: Never say electron microscopes are better simply because they "zoom in more." The CCEA mark scheme specifically requires you to state that electron microscopes have a higher resolution because the wavelength of an electron beam is much shorter than the wavelength of visible light.
The Magnification Formula
To calculate magnification, use the standard formula triangle:
\(\text{Magnification } (M) = \frac{\text{Image Size } (I)}{\text{Actual Size } (A)}\)
\(\text{Actual Size } (A) = \frac{\text{Image Size } (I)}{\text{Magnification } (M)}\)
\(\text{Image Size } (I) = \text{Actual Size } (A) \times \text{Magnification } (M)\)
Unit Conversion Rules: Before doing any calculation, you must convert all measurements into the same units (usually micrometres, \(\mu\text{m}\)):
• \(1\text{ millimetre (mm)} = 1000\text{ micrometres } (\mu\text{m})\) (multiply by \(1000\))
• \(1\text{ micrometre } (\mu\text{m}) = 1000\text{ nanometres (nm)}\) (multiply by \(1000\))
• To convert backwards (\(\text{nm} \rightarrow \mu\text{m} \rightarrow \text{mm}\)), divide by \(1000\) at each step.
Comparing Types of Microscopes
1. Light (Optical) Microscope:
• Uses beams of visible light and glass lenses.
• Resolution is limited to approximately \(200\text{ nm}\) (\(0.2\,\mu\text{m}\)) due to the longer wavelength of light.
• Maximum useful magnification is around \(\times 1500\).
• Advantages: Can view living specimens; specimens can be observed in their natural colour.
• Disadvantages: Cannot resolve fine internal cell ultrastructure (e.g., ribosomes, details of cristae).
2. Transmission Electron Microscope (TEM):
• A beam of electrons passes through an ultra-thin, stained specimen.
• Extremely high resolution (\(\approx 0.1\text{–}0.5\text{ nm}\)) due to the short wavelength of electrons.
• Produces 2D high-magnification images of internal organelle ultrastructure.
3. Scanning Electron Microscope (SEM):
• A beam of electrons is scanned across the gold-coated surface of the specimen, and reflected electrons are collected.
• Produces dramatic 3D images of external topography and surfaces.
Limitations of Electron Microscopy:
• Specimens must be viewed inside a vacuum, meaning specimens must be dead and dehydrated.
• Complex preparation steps can produce structural distortions called artefacts.
• Images are in black and white (any colour seen in micrographs is false/added colour).
Microscope Calibration: Graticules and Stage Micrometers
To measure the true size of a cell under a light microscope, you calibrate your viewing field using two tools:
1. Eyepiece Graticule: A glass disc etched with an arbitrary scale of 0 to 100 units. It does not have real units (it is measured in eyepiece units, epu) and does not change size when changing magnification.
2. Stage Micrometer: A precision slide with a known, etched microscopic ruler (typically a \(1\text{ mm}\) scale divided into 100 divisions, meaning \(1\text{ division} = 10\,\mu\text{m}\) or \(0.01\text{ mm}\)).
Calibration Procedure:
• Superimpose the eyepiece graticule scale over the stage micrometer scale at a specific magnification.
• Count how many eyepiece units correspond to a known distance on the stage micrometer.
• Calculate the value of \(1\text{ epu}\) (e.g., if \(10\text{ epu} = 100\,\mu\text{m}\), then \(1\text{ epu} = 10\,\mu\text{m}\)).
• Crucial Rule: If you switch objective lenses (e.g., from \(\times 10\) to \(\times 40\)), you must recalibrate because the field of view magnifies, but the graticule scale remains the same physical size.
Section Takeaway: Always remember \(M = \frac{I}{A}\), convert measurements to the same units (\(\mu\text{m}\)) first, and remember that higher resolution in electron microscopes is due to the shorter wavelength of electrons.
---2. Eukaryotic Cell Ultrastructure
Eukaryotic cells are compartmentalised into membrane-bound structures called organelles. Think of a eukaryotic cell as an organised manufacturing factory, where each organelle has a distinct workstation role.
The Nucleus
• Structure: Enclosed by a double-membrane called the nuclear envelope, which is perforated by nuclear pores. Contains chromatin (DNA wrapped around histone proteins). Contains a dense sub-region called the nucleolus.
• Function: Controls gene expression and cellular activities. Nuclear pores allow the passage of large molecules such as messenger RNA (mRNA) and ribosomal subunits out into the cytoplasm. The nucleolus is the site of ribosomal RNA (rRNA) synthesis and ribosome assembly.
Endoplasmic Reticulum (ER)
• Rough Endoplasmic Reticulum (RER): A series of flattened, fluid-filled membrane sacs called cisternae, studded with \(80\text{S}\) ribosomes on the outer surface. Folds, processes, and transports synthesized proteins.
• Smooth Endoplasmic Reticulum (SER): A tubular membrane network lacking ribosomes. Synthesizes, stores, and transports lipids and carbohydrates.
The Golgi Apparatus
• Structure: A stack of curved, flattened membrane-bound sacs (cisternae) constantly receiving and budding off vesicles.
• Function: Modifies proteins and lipids (e.g., adding carbohydrate chains to make glycoproteins), packages molecules into Golgi vesicles for transport or secretion via exocytosis, and produces lysosomes.
Lysosomes
• Structure: Membrane-bound spherical vesicles formed by the Golgi apparatus containing acidic hydrolytic enzymes (lysozymes).
• Function: Hydrolyses material ingested by phagocytic cells; breaks down damaged organelles (autophagy); digests dead cells after apoptosis (autolysis).
Mitochondria
• Structure: Double-membraned organelle. The outer membrane is smooth, while the inner membrane is deeply folded into extensions called cristae. The central fluid interior is the matrix, which contains circular mitochondrial DNA, \(70\text{S}\) ribosomes, and respiratory enzymes.
• Function: Site of aerobic respiration and ATP production. The cristae provide a large surface area for enzymes and electron carriers involved in the electron transport chain.
Ribosomes
• Structure: Non-membrane-bound complexes consisting of ribosomal RNA (rRNA) and proteins, formed of one large and one small subunit.
• Types: \(80\text{S}\) ribosomes (approx. \(25\text{ nm}\) diameter) are found in eukaryotic cytoplasm and bound to RER. Smaller \(70\text{S}\) ribosomes are found inside prokaryotes, mitochondria, and chloroplasts.
• Function: Site of protein synthesis (translation).
Chloroplasts (Plant & Algal Cells)
• Structure: Surrounded by a double membrane (chloroplast envelope). Internally contains flattened membrane discs called thylakoids stacked into piles termed grana (singular: granum), linked together by intergranal lamellae. The fluid surrounding the grana is the stroma.
• Function: Site of photosynthesis. Thylakoid membranes contain chlorophyll for the light-dependent stage; the stroma contains enzymes (like Rubisco), circular DNA, starch granules, and \(70\text{S}\) ribosomes for the light-independent stage.
Vacuole and Tonoplast
• Structure: A large, permanent fluid-filled compartment found in plant cells bounded by a single selectively permeable membrane called the tonoplast. It contains cell sap (water, mineral ions, sugars, and amino acids).
• Function: Supports the plant by maintaining cell turgor pressure; stores nutrients and wastes.
Cell Wall
• Plant Cell Wall: Consists of high-tensile cellulose microfibrils embedded in a polysaccharide matrix. Connected to neighbouring plant cells by the middle lamella (made of calcium pectate). Perforated by channels called plasmodesmata, which allow cytoplasmic transport and communication between adjacent cells.
• Fungal Cell Wall: Made of the polysaccharide chitin.
QWC Spelling Alert: Pay close attention to spelling in your written answers:
• Cristae (mitochondrial folds) vs. Cisternae (ER and Golgi sacs)
• Tonoplast (vacuole membrane)
• Plasmodesmata (intercellular cytoplasmic channels)
3. Prokaryotic Cells vs. Eukaryotic Cells
Prokaryotes (such as bacteria) are simpler, evolutionary older, and smaller (typically \(1\text{–}10\,\mu\text{m}\)) than eukaryotic cells.
Key Structural Features of Prokaryotes
• No membrane-bound organelles: No nucleus, mitochondria, chloroplasts, ER, or Golgi apparatus.
• Genetic Material: A single, circular double-stranded DNA molecule that floats freely in a region called the nucleoid (it is naked, meaning it is not bound to histone proteins). Many bacteria also contain small, circular accessory rings of DNA called plasmids.
• Ribosomes: Contain only smaller \(70\text{S}\) ribosomes.
• Cell Wall: Always composed of murein (peptidoglycan), never cellulose or chitin.
• Optional Structures:
- Slime Capsule: A protective outer layer that prevents dehydration and shields against immune attack.
- Flagella: Rigid rotating protein structures used for locomotion.
- Pili / Fimbriae: Hair-like protein projections used for surface attachment and genetic exchange.
Summary Comparison Table
Eukaryotes: True nucleus with nuclear envelope; DNA linear and associated with histones; membrane-bound organelles present; \(80\text{S}\) ribosomes in cytoplasm; cell wall made of cellulose (plants) or chitin (fungi) or absent (animals).
Prokaryotes: No nucleus (naked circular DNA in nucleoid); plasmids present; no membrane-bound organelles; \(70\text{S}\) ribosomes; cell wall made of murein (peptidoglycan).
Memory Tip (Endosymbiotic link): Mitochondria and chloroplasts have their own \(70\text{S}\) ribosomes and circular DNA, just like bacteria!
---4. Viruses
Viruses are unique biological entities because they are acellular (not made of cells) and non-living.
Virus Structure
• Size: Very small, ranging from approximately \(20\text{–}300\text{ nm}\) (much smaller than bacteria).
• Genetic Core: Contains nucleic acid, which can be single-stranded or double-stranded DNA or RNA.
• Capsid: A protective outer protein shell enclosing the genetic material.
• Envelope (in some viruses): An outer lipid bilayer membrane derived from the host cell's membrane (e.g., in HIV or influenza).
• Attachment Glycoproteins: Surface proteins that bind to specific complementary receptors on host cell surfaces to enable infection.
Section Takeaway: Viruses do not carry out metabolic reactions, do not have organelles or ribosomes, and can only replicate inside a living host cell.
---5. Cell Fractionation and Ultracentrifugation
Cell fractionation is the technique used to separate and isolate organelles based on their size and density, allowing their individual biochemistry to be studied.
Stage 1: Homogenisation (Breaking the Cells Open)
Tissue is placed in a blender (homogeniser) with an aqueous solution. To protect the organelles from damage during this step, the solution must meet three vital conditions:
1. Ice-Cold: Low temperature slows down and inhibits destructive enzyme activity (such as autolytic hydrolytic enzymes released from broken lysosomes).
2. Isotonic: The solution must have the same water potential as the organelles to prevent net movement of water by osmosis, preventing organelles from bursting (osmotic lysis) or shrinking (crenation).
3. Buffered: Maintains a constant, stable pH so that organelle proteins and enzymes do not denature.
Stage 2: Filtration
The resulting homogenate is poured through a fine mesh filter to remove intact, unbroken cells and large tissue debris.
Stage 3: Differential Centrifugation
The filtered homogenate is spun in a centrifuge at progressively higher speeds and gravitational forces:
1. Low Speed: The heaviest, densest organelles sediment to the bottom to form a pellet. This first pellet consists of Nuclei.
2. The remaining liquid above the pellet, called the supernatant, is transferred to a new tube and spun at a Medium Speed. The second pellet consists of Mitochondria (and Chloroplasts if plant tissue is used).
3. The supernatant is spun at a Higher Speed: The third pellet consists of Lysosomes and peroxisomes.
4. The supernatant is spun at a Very High Speed: The fourth pellet consists of Endoplasmic Reticulum and Golgi fragments (microsomes).
5. The supernatant is spun at the Highest Speed (Ultracentrifugation): The final, lightest pellet consists of Ribosomes.
Mnemonic to Remember Sedimentation Order:
Naughty Monkeys Like Eating Raspberries
(Nuclei \(\rightarrow\) Mitochondria/Chloroplasts \(\rightarrow\) Lysosomes \(\rightarrow\) ER/Golgi \(\rightarrow\) Ribosomes)
Quick Review: Common Exam Pitfalls
• Forgetting to convert units: Always ensure Image and Actual sizes are in the same units (convert everything to \(\mu\text{m}\)!) before using \(M = \frac{I}{A}\).
• Confusing Graticule vs Micrometer: An eyepiece graticule has arbitrary units and must be calibrated against a stage micrometer for each objective lens magnification.
• Bacterial Cell Walls: Bacterial cell walls are made of murein / peptidoglycan, NOT cellulose.
• Fractionation Conditions: Make sure you match each condition to its correct reason (Ice-cold = reduce enzyme action; Isotonic = prevent osmotic damage; Buffered = maintain pH to prevent protein denaturation).
• Ribosomes in Organelles: Remember that while eukaryotes have \(80\text{S}\) ribosomes in their cytoplasm, mitochondria and chloroplasts contain \(70\text{S}\) ribosomes.