Cells

Welcome to the World of Cells!

Welcome to one of the most exciting foundations of AS Level Biology! Everything alive—from the giant blue whale to the tiniest bacterium on your skin—is made of cells. Think of cells as the ultimate building blocks of life, or microscopic factories humming with activity \(24\) hours a day.

Don't worry if cell ultrastructure feels a bit overwhelming with all of its technical names. We are going to break down every organelle step-by-step, use everyday analogies, and master the calculations together. By the end of these notes, you will know exactly what makes cells tick and how to ace your CCEA exam questions!

1. Microscopy: How We Study Cells

Cells are far too small to see with the naked eye, so biologists rely on microscopes. Before we look inside a cell, we need to understand the tools used to observe them.

Magnification vs. Resolution

These two terms are frequently confused in exams, but they describe very different things:

• Magnification: How many times larger an image appears compared to the actual real-life size of the specimen.

• Resolution (Resolving Power): The ability to distinguish between two separate points that are close together. A higher resolution gives a clearer, sharper image with finer detail.

Analogy: Imagine zooming in on a low-quality digital photo. The image gets bigger (high magnification), but it becomes blurry and pixelated because the resolution is low!

Types of Microscopes

1. Light (Optical) Microscope:

• Uses visible light and glass lenses to focus the image.

• Maximum practical magnification: approximately \(\times 1500\).

• Maximum resolution: approximately \(200\text{ nm}\) (limited by the wavelength of light).

• Advantages: Can view living specimens, cheap, portable, and allows natural colours or simple stains to be seen.

• Disadvantages: Low resolution and magnification compared to electron microscopes; cannot see fine internal structures (ultrastructure) of small organelles like ribosomes.

2. Transmission Electron Microscope (TEM):

• Beams electrons through a very thin section of a specimen.

• Maximum resolution: up to \(0.5\text{ nm}\) (electrons have a much shorter wavelength than visible light).

• Maximum magnification: up to \(\times 500{,}000\) or more.

• Advantages: Extremely high resolution reveals 2D internal ultrastructure of organelles.

• Disadvantages: Specimens must be dead (viewed in a vacuum), preparation is complex and can introduce artifacts (features that look like organelles but are actually caused by preparation damage), and images are black and white.

3. Scanning Electron Microscope (SEM):

• Bounces a beam of electrons off the surface of a specimen.

• Resolution: approximately \(3\text{ nm}\) to \(10\text{ nm}\) (lower than TEM, but higher than optical).

• Advantages: Produces stunning 3D images of cell surfaces.

• Disadvantages: Cannot view internal structures, specimens must be dead, expensive, and black and white (often false-coloured digitally).

Microscopy Calculations (\(I = A \times M\))

A classic exam calculation uses the formula triangle linking Image size (\(I\)), Actual size (\(A\)), and Magnification (\(M\)):

\(M = \frac{I}{A}\)

\(A = \frac{I}{M}\)

\(I = A \times M\)

Memory Trick: Remember the word "AIM" \(\rightarrow\) Actual \(\times\) Image / Magnification, or visualize the triangle with \(I\) on top and \(A \times M\) on the bottom.

Converting Units (Crucial Step!):

Always convert all measurements to the same units (usually micrometres, \(\mu\text{m}\)) before doing your calculation:

• Centimetres (\(\text{cm}\)) to Millimetres (\(\text{mm}\)): \(\times 10\)

• Millimetres (\(\text{mm}\)) to Micrometres (\(\mu\text{m}\)): \(\times 1000\)

• Micrometres (\(\mu\text{m}\)) to Nanometres (\(\text{nm}\)): \(\times 1000\)

Worked Example: A cell has an image diameter of \(24\text{ mm}\) under a microscope magnification of \(\times 400\). What is its actual size in \(\mu\text{m}\)?

Step 1: Convert \(I\) to \(\mu\text{m}\): \(24\text{ mm} \times 1000 = 24{,}000\text{ \mu m}\).

Step 2: Use formula: \(A = \frac{I}{M} = \frac{24{,}000}{400} = 60\text{ \mu m}\).

Calibrating the Eyepiece Graticule

An eyepiece graticule is a small transparent ruler fitted into the microscope eyepiece. It has arbitrary units (e.g., 0–100 subdivisions) that do not change scale when you switch objective lenses. To find out what each unit measures in real life, we calibrate it using a stage micrometer (a slide with an accurate, known scale, typically \(1\text{ mm}\) divided into \(100\) subdivisions, where each small division = \(10\text{ \mu m}\)).

Step-by-Step Calibration:

1. Line up the zero marks of the eyepiece graticule and the stage micrometer.

2. Find a point further along where lines on both scales line up exactly.

3. Count the number of eyepiece units (epu) and calculate the corresponding distance on the stage micrometer.

4. Divide the actual distance by the number of epu to find the value of 1 epu.

Example: If \(20\) eyepiece units \(= 10\) stage units (\(10 \times 10\text{ \mu m} = 100\text{ \mu m}\)), then \(1\text{ epu} = \frac{100\text{ \mu m}}{20} = 5\text{ \mu m}\).

Key Takeaways: Microscopy

• Resolution is clarity and detail; magnification is size.

• Light microscopes view live specimens in colour; electron microscopes have much higher resolution but require dead specimens in a vacuum.

• Remember \(I = A \times M\) and always convert measurements into the same units before calculating!

2. Eukaryotic Cell Ultrastructure

Eukaryotic cells are complex cells containing a membrane-bound nucleus and membrane-bound organelles (like mitochondria and chloroplasts). Animals, plants, fungi, and protoctists are all eukaryotes.

Analogy: Think of a eukaryotic cell as a factory town. Each organelle is a dedicated workshop specialized to perform one specific job smoothly and efficiently.

Organelles and Their Functions

1. The Nucleus:

• Structure: Enclosed by a double membrane called the nuclear envelope containing nuclear pores. Inside is chromatin (DNA wound around histone proteins) and a dense region called the nucleolus.

• Function: Controls cell activities by regulating gene expression and protein synthesis. Nuclear pores allow substances (like mRNA) to leave the nucleus. The nucleolus makes ribosomal RNA (rRNA) and assembles ribosome subunits.

2. Mitochondrion (plural: Mitochondria):

• Structure: Surrounded by a double membrane. The inner membrane folds inward to form shelf-like projections called cristae, which project into an interior fluid called the matrix. Contains its own circular DNA and \(70\text{S}\) ribosomes.

• Function: The site of aerobic respiration, producing ATP (the universal energy currency of cells). Cristae provide a large surface area for enzymes involved in ATP synthesis.

3. Ribosomes:

• Structure: Tiny, non-membrane-bound particles made of rRNA and protein. Eukaryotes have larger \(80\text{S}\) ribosomes in the cytoplasm and on the RER, and \(70\text{S}\) ribosomes inside mitochondria and chloroplasts.

• Function: The site of translation / protein synthesis.

4. Rough Endoplasmic Reticulum (RER):

• Structure: A network of flattened, membrane-bound sacs (cisternae) studded with ribosomes on the outer surface, continuous with the outer nuclear membrane.

• Function: Folds and transports proteins made by the attached ribosomes, packing them into transport vesicles.

5. Smooth Endoplasmic Reticulum (SER):

• Structure: A tubular network of membrane cisternae without ribosomes.

• Function: Synthesizes, stores, and transports lipids and carbohydrates (e.g., steroids, phospholipids).

6. Golgi Body (Golgi Apparatus):

• Structure: A stack of flattened, curved, membrane-bound sacs surrounded by small spherical vesicles.

• Function: The "post office" of the cell. It modifies proteins (e.g., adding carbohydrate chains to make glycoproteins), sorts them, and packages them into Golgi vesicles for transport to other organelles or for secretion outside the cell (exocytosis).

7. Lysosomes:

• Structure: Spherical vesicles formed by the Golgi body, containing hydrolytic (digestive) enzymes (lysozymes), surrounded by a single thick membrane.

• Function: Digest worn-out organelles, break down engulfed pathogens (in phagocytic white blood cells), and carry out self-destruction of damaged cells (autolysis).

8. Centrioles and Microtubules:

• Structure: Pairs of hollow cylinders made of tubulin protein triplets, found in animal cells.

• Function: Form the spindle fibres during cell division (mitosis/meiosis) to move chromosomes.

Plant-Specific Organelles

1. Chloroplasts:

• Structure: Double-membrane biconvex organelle. Internally contains stacks of flattened, fluid-filled thylakoids called grana (singular: granum), linked by intergranal lamellae, surrounded by a fluid gel called the stroma. Also contains circular DNA and \(70\text{S}\) ribosomes.

• Function: The site of photosynthesis. Thylakoid membranes contain chlorophyll to trap light energy for the light-dependent stage; the stroma contains enzymes (like RuBisCO) for the light-independent stage.

2. Cell Wall:

• Structure: Strong outer layer composed of bundles of cellulose microfibrils embedded in a pectin matrix. Adjacent cells are glued together by the middle lamella and communicate through fine cytoplasmic channels called plasmodesmata.

• Function: Provides mechanical strength and structural support, prevents the cell from bursting when water enters by osmosis (turgidity), and is fully permeable to water and dissolved solutes.

3. Large Permanent Vacuole:

• Structure: Fluid-filled sac surrounded by a selectively permeable membrane called the tonoplast.

• Function: Contains cell sap (water, mineral ions, sugars, pigments); maintains cell turgidity and serves as temporary storage.

The Pathway of Protein Synthesis and Secretion

How do organelles coordinate together to make and export a protein (like an enzyme or hormone)? Follow this step-by-step assembly line:

1. Nucleus: DNA is transcribed into mRNA, which exits via a nuclear pore.

2. Ribosome / RER: mRNA binds to a ribosome on the RER, where the protein is synthesized and threaded into the RER lumen to be folded.

3. Transport Vesicle: The protein is pinched off in a transport vesicle and moves toward the Golgi body.

4. Golgi Body: The vesicle fuses with the Golgi cisternae; the protein is modified (e.g., converted to a glycoprotein) and packaged.

5. Secretory Vesicle: A secretory vesicle pinches off from the Golgi, moves along the cytoskeleton to the cell surface membrane, and fuses with it to release the protein outside the cell by exocytosis.

Key Takeaways: Eukaryotic Cells

• Nucleus stores genetic code; Ribosomes + RER build and fold proteins; Golgi modifies and exports them.

• Mitochondria produce ATP via aerobic respiration.

• Plant cells uniquely have cellulose walls, chloroplasts, and a large permanent vacuole with a tonoplast.

3. Prokaryotic Cells

Prokaryotic cells (e.g., bacteria) are significantly smaller and structurally simpler than eukaryotic cells. They lack membrane-bound organelles and do not have a true nucleus.

Structure of a Bacterium

• Nucleoid (Circular DNA): A single, long, circular strand of DNA floating free in the cytoplasm. Not enclosed in a membrane and not associated with histone proteins ("naked DNA").

• Plasmids: Small, circular, independent loops of DNA that can replicate separately. Often carry antibiotic resistance genes and can be transferred between bacteria.

• Ribosomes (\(70\text{S}\)): Smaller than eukaryotic \(80\text{S}\) ribosomes; site of protein synthesis.

• Cell Wall: Made of peptidoglycan (also called murein), NOT cellulose. Protects against osmotic lysis.

• Plasma Membrane: Phospholipid bilayer controlling entry and exit of substances.

• Slime Capsule (in some species): Outer protective mucus layer that prevents dehydration and shields against white blood cells.

• Flagellum (in some species): Rigid, rotating protein structure used for locomotion.

• Pili (in some species): Hair-like attachments used for sticking to surfaces or transferring plasmids during conjugation.

Eukaryotes vs. Prokaryotes: Quick Comparison

• Nucleus: Eukaryotes have a membrane-bound nucleus; Prokaryotes have no nucleus (free circular DNA in nucleoid).

• DNA: Eukaryotes have linear DNA wrapped around histones; Prokaryotes have circular naked DNA (plus plasmids).

• Ribosomes: Eukaryotes have larger \(80\text{S}\) ribosomes in cytoplasm; Prokaryotes have smaller \(70\text{S}\) ribosomes.

• Membrane-bound organelles: Present in Eukaryotes (e.g., mitochondria, ER, Golgi); Completely absent in Prokaryotes.

• Cell Wall: Eukaryotic plants have cellulose (fungi have chitin); Prokaryotes have peptidoglycan (murein).

• Size: Eukaryotes are larger (typically \(10\)–\(100\text{ \mu m}\)); Prokaryotes are much smaller (typically \(0.5\)–\(5\text{ \mu m}\)).

Did You Know?

Mitochondria and chloroplasts contain their own circular DNA and \(70\text{S}\) ribosomes—just like bacteria! The Endosymbiotic Theory suggests they were once free-living prokaryotes that were engulfed by ancestral eukaryotic cells billions of years ago!

4. Viruses: Acellular Structures

Viruses are acellular—meaning they are not made of cells and are non-living biological entities. They cannot perform metabolic reactions or reproduce on their own; they are obligate intracellular parasites that hijack a host cell's machinery to multiply.

Structure of a Virus

• Genetic Material: A core containing nucleic acid—either DNA or RNA (single- or double-stranded), but never both.

• Capsid: A protective outer coat made of repeating protein subunits called capsomeres.

• Attachment Proteins: Surface proteins / glycoproteins that identify and bind to specific receptor proteins on host cells.

• Lipid Envelope (some viruses, e.g., HIV, Influenza): Stolen lipid membrane derived from the host cell during exit.

5. Levels of Biological Organisation

In multicellular organisms, cells do not work in isolation. They are organised hierarchically to carry out life functions efficiently:

1. Specialized Cells: The basic structural and functional unit (e.g., squamous epithelial cell, red blood cell, palisade mesophyll cell).

2. Tissues: A collection of similar, specialized cells working together to perform a specific function (e.g., epithelial tissue covering body surfaces, xylem tissue transporting water and mineral ions in plants).

3. Organs: A distinct structural unit composed of several different tissues grouped together to perform a major physiological function (e.g., the stomach contains epithelial, muscular, and glandular tissues; a plant leaf contains epidermal, mesophyll, and vascular tissues).

4. Organ Systems: A group of organs cooperating to carry out complex body functions (e.g., the digestive system, circulatory system).

5. Organism: The complete living individual made of coordinated organ systems.

Common Exam Pitfalls & How to Avoid Them

• Confusing \(70\text{S}\) and \(80\text{S}\) ribosomes: Remember that prokaryotes, mitochondria, and chloroplasts have \(70\text{S}\), while the eukaryotic cytoplasm/RER has \(80\text{S}\).

• Cell Wall mix-ups: Plants = cellulose; Fungi = chitin; Bacteria = peptidoglycan / murein. Never say bacteria have cellulose walls!

• Calling viruses cells: Viruses are strictly acellular particles with no cytoplasm, organelles, or cell membrane.

• Forgetting unit conversions: In microscopy calculations, always convert all values to \(\mu\text{m}\) before dividing!

Final Review Checklist

Can you answer these key questions before your exam?

1. Can you write down the \(I = A \times M\) equation and rearrange it to find actual size and magnification?

2. Can you list four structural differences between a bacterium and a palisade cell?

3. Can you trace the journey of an enzyme from its synthesis on the RER to its secretion outside the cell?

4. Can you describe how to calibrate an eyepiece graticule using a stage micrometer?

Keep reviewing these notes, practice your diagrams and calculations, and you will be completely prepared for this section in AS Level Biology!