Cells, membranes, the microscope, DNA and inheritance, microorganisms, blood and the immune system: the biology every lab career builds on.

Biology Fundamentals

## Why it matters

Every sample that reaches a biology or clinical lab is made of cells or comes from them: a blood smear, a bacterial culture, a cell line growing in a flask, a tissue section. When a technician looks down a microscope, runs a cell count or extracts DNA, they are working with the parts of the cell. Knowing what those parts are, and what they do, tells you why a protocol says "lyse the membrane first" or why a stain lights up the nucleus.

## The core idea: two kinds of cell

All living cells share four things: a **plasma membrane** that encloses them, **cytoplasm** (the watery interior), **ribosomes** that build proteins, and **DNA** that holds the instructions. Beyond that, cells come in two broad designs.

- **Prokaryotic cells** (bacteria and archaea) have no nucleus. Their DNA sits in a region called the **nucleoid**, usually as one circular chromosome, often with small extra circles called **plasmids**. Most have a rigid **cell wall** outside the membrane. They are small, typically 1 to 5 micrometres (µm) long.
- **Eukaryotic cells** (animals, plants, fungi, protists) keep their DNA inside a **nucleus** and have many membrane-bound compartments called **organelles**. They are larger, typically 10 to 100 µm.

## A tour of the eukaryotic cell

Think of the cell as a small factory. Each organelle has a job:

| Organelle | Job |
|---|---|
| **Nucleus** | Stores DNA and controls which genes are used. The **nucleolus** inside it makes ribosome parts. |
| **Ribosomes** | Read messenger RNA and join amino acids into proteins. Free in the cytoplasm or attached to the rough ER. |
| **Rough endoplasmic reticulum (ER)** | Membrane network studded with ribosomes; makes proteins that will be exported or placed in membranes. |
| **Smooth ER** | Makes lipids and helps detoxify drugs (large in liver cells). |
| **Golgi apparatus** | Modifies, sorts and packages proteins from the ER into vesicles, the cell's "shipping department". |
| **Mitochondria** | Release energy from food by aerobic respiration and make ATP. They have their own small DNA. |
| **Lysosomes** | Bags of digestive enzymes that break down worn-out parts and engulfed material (animal cells). |
| **Cytoskeleton** | Protein filaments that give shape, move organelles and let cells crawl or divide. |
| **Plasma membrane** | Controls what enters and leaves (next lesson). |

Plant cells add three features: a **cell wall** made of cellulose, **chloroplasts** that capture light for photosynthesis, and a large **central vacuole** that stores water and keeps the cell firm.

## Worked example: following one protein

Antibodies are proteins made by immune B cells (plasma cells) and released into the blood. Here is the route one antibody takes:

1. In the **nucleus**, the antibody gene is copied into messenger RNA.
2. The mRNA leaves through a nuclear pore and is read by ribosomes on the **rough ER**, which feed the new protein chain into the ER.
3. The protein folds in the ER and is carried in a vesicle to the **Golgi**, where sugar groups are added.
4. A vesicle from the Golgi fuses with the **plasma membrane** and releases the antibody outside the cell.
5. **Mitochondria** supply the ATP for all of these steps.

Plasma cells are packed with rough ER for exactly this reason: they are antibody factories. Structure follows function, which is a useful rule throughout biology.

## Worked example: why it matters at the bench

A protocol for extracting DNA from cultured human cells starts with a **lysis buffer** containing a detergent. The detergent dissolves the lipid plasma membrane and the nuclear membrane so the DNA is released. A protocol for bacteria often adds an enzyme such as lysozyme first, because the bacterial **cell wall** would otherwise protect the cells from the detergent. The difference in the protocol comes straight from the difference in cell structure.

## Common mistakes

- **Saying bacteria have no DNA organisation.** They have no nucleus, but their DNA is organised in the nucleoid.
- **Confusing the cell wall and the cell membrane.** Plants, fungi and most bacteria have both; animal cells have only the membrane.
- **Thinking only plants have mitochondria or only animals do.** Plants have both chloroplasts and mitochondria.
- **Mixing up sizes.** A typical bacterium is around a tenth the length of a typical human cell; viruses (module 3) are smaller still.

## Quick recap

- All cells have a membrane, cytoplasm, ribosomes and DNA.
- Prokaryotes have no nucleus or membrane-bound organelles; eukaryotes do.
- Nucleus stores DNA, ribosomes make proteins, ER and Golgi process and ship them, mitochondria make ATP, lysosomes digest.
- Plant cells add a cell wall, chloroplasts and a large vacuole.
- Lab protocols are designed around these structures.


Name the main organelles of animal, plant and bacterial cells and say what each one does.

Cell structure

Introduction to Cells: The Grand Cell Tour

Eukaryopolis - The City of Animal Cells: Crash Course Biology #4

## Why it matters

The cell membrane decides what gets in and what stays out. That matters at the bench every day. Red blood cells burst if you dilute a blood sample in pure water. Cultured cells shrink if their medium is too salty. Drugs only work if they can reach their target inside or on the cell. Understanding membrane transport tells you why lab solutions are made **isotonic** (the same overall solute concentration as the cell) and why the exact recipe of a buffer matters.

## The core idea: a selective barrier

The plasma membrane is a **phospholipid bilayer**. Each phospholipid has a water-loving (hydrophilic) head and two water-fearing (hydrophobic) tails. In water they line up in two layers, heads out and tails in. Proteins float in this layer, which is why it is called the **fluid mosaic model**.

The oily middle is the key. Small, uncharged molecules such as oxygen and carbon dioxide slip through easily. Water crosses slowly on its own and much faster through channel proteins called **aquaporins**. Ions (Na⁺, K⁺, Cl⁻) and larger polar molecules such as glucose cannot cross the oily core without help from proteins.

## Passive transport: no energy needed

Passive transport moves substances **down their concentration gradient**, from where they are more concentrated to where they are less concentrated. The cell spends no ATP.

- **Simple diffusion:** molecules spread out through the bilayer by random motion. Example: oxygen moving from the blood into a muscle cell.
- **Facilitated diffusion:** a channel or carrier protein provides a path, but the direction is still downhill. Example: glucose entering red blood cells through the GLUT1 carrier.
- **Osmosis:** the diffusion of **water** across a membrane that solutes cannot cross. Water moves toward the side with **more dissolved solute** (less free water).

## Osmosis in practice: tonicity

Tonicity describes a solution compared with the inside of a cell.

| Outside solution | Water moves | Animal cell (red blood cell) | Plant cell |
|---|---|---|---|
| **Hypotonic** (fewer solutes outside) | into the cell | swells and may burst (**lysis**) | becomes firm (turgid); the wall stops it bursting |
| **Isotonic** (equal) | no net movement | normal shape | limp (flaccid) |
| **Hypertonic** (more solutes outside) | out of the cell | shrinks and crinkles (**crenation**) | membrane pulls away from the wall (**plasmolysis**) |

**Worked example.** Physiological saline is 0.9% sodium chloride, which is roughly isotonic with human blood. That is why it is used to dilute blood cells for counting and as a base for many cell-washing buffers. Mix red cells with distilled water instead and they swell and lyse within minutes, releasing haemoglobin: the solution turns clear red. Mix them with 3% salt and they crenate. A lab that sees unexpected lysis in a sample checks the diluent first.

## Active transport: energy needed

Active transport moves substances **against** their gradient, from low to high concentration. It needs energy, usually ATP.

The best-known example is the **sodium-potassium pump** (Na⁺/K⁺-ATPase). For each ATP it uses, it pushes 3 Na⁺ out of the cell and brings 2 K⁺ in. This keeps sodium low and potassium high inside cells, which nerves and muscles depend on. It is also why a blood sample left unseparated for too long can show a falsely high potassium result: as the cells run out of energy, the pumps slow and potassium leaks out of the cells into the serum.

Cells also move large particles in bulk:

- **Endocytosis:** the membrane folds inward to take material in. **Phagocytosis** ("cell eating") is how white blood cells engulf bacteria.
- **Exocytosis:** vesicles fuse with the membrane to release their contents, as in the antibody example from the last lesson.

## Comparing the methods

| Method | Direction | Needs a protein? | Needs ATP? | Example |
|---|---|---|---|---|
| Simple diffusion | down gradient | no | no | O₂, CO₂ |
| Facilitated diffusion | down gradient | yes (channel or carrier) | no | glucose via GLUT1, water via aquaporins |
| Osmosis | water toward more solute | sometimes (aquaporins) | no | red cells in water |
| Active transport | against gradient | yes (pump) | yes | Na⁺/K⁺ pump |
| Endo/exocytosis | bulk | membrane vesicles | yes | phagocytosis, secretion |

## Common mistakes

- **Saying water moves toward more water.** In osmosis water moves toward the side with *more solute*.
- **Thinking facilitated diffusion uses energy.** It uses a protein but no ATP; the gradient drives it.
- **Mixing up hypo- and hypertonic.** "Hypo" means under: fewer solutes outside, so water rushes in.
- **Forgetting the plant cell wall.** Plant cells in pure water do not burst; the wall pushes back.

## Quick recap

- The phospholipid bilayer lets small nonpolar molecules through and blocks ions and large polar ones.
- Passive transport (diffusion, facilitated diffusion, osmosis) runs down the gradient with no ATP.
- Active transport pumps against the gradient using ATP; the Na⁺/K⁺ pump is the classic example.
- Lab solutions are made isotonic (such as 0.9% saline) so cells keep their shape.


Explain how substances cross cell membranes by diffusion, osmosis, facilitated diffusion and active transport.

Membranes and transport

Cell Transport

In Da Club - Membranes & Transport: Crash Course Biology #5

Carry the microscope with one hand on the arm and one under the base, set it on a flat table and plug it in away from water. Turn the light on at low brightness.

Rotate the lowest-power objective (usually 4x) into place and lower the stage fully with the coarse focus knob.

Prepare a specimen: lay a thin piece of onion skin (or a small letter "e" cut from newsprint) flat on a clean slide, add one drop of tap water, and lower a cover slip at an angle to avoid bubbles. Or use a prepared slide.

Clip the slide on the stage with the specimen over the hole. Looking from the side, raise the stage until the objective is close to the slide but not touching it.

Look through the eyepiece and lower the stage slowly with the coarse knob until the image appears, then sharpen it with the fine knob. Adjust the light or diaphragm for good contrast. If you used the letter "e", note which way it appears and how it moves when you slide it.

Measure the field of view at 4x: place a clear plastic ruler on the stage and count how many millimetre marks fit across the circle. Write it down (for example 4.5 mm = 4,500 µm).

Calculate the field of view at higher power: new field = 4x field × (4 ÷ new objective). For a 10x objective with a 4.5 mm field at 4x, that is 4,500 × 0.4 = 1,800 µm.

Centre a cell, switch to 10x and refocus with the fine knob only. Estimate how many cells fit across the field and divide: cell length ≈ field diameter ÷ number of cells. Record your answer in µm.

Calculate the total magnification you used (eyepiece × objective, for example 10 × 10 = 100x) and write it next to your measurement.

Finish: return to the lowest objective, lower the stage, remove the slide, put kitchen specimens in the bin, wipe the slide, and turn the light off before covering the microscope.

> **Awareness level only.** This lesson teaches how a microscope works and how to measure with one on safe specimens. In a real lab, handling patient samples, cultures or stains requires the training your employer or institution provides, and you work under supervision until you are signed off.

## Why it matters

The light microscope is still one of the most used instruments in biology and clinical labs. Technicians check cell cultures for health and contamination, count cells, read Gram stains and examine blood smears. Doing it well means getting a sharp image quickly without damaging the slide or the lens, and reporting sizes in the right units.

## The core idea: magnification and resolution

A **compound light microscope** uses two lenses in series:

- the **eyepiece** (ocular), usually 10x
- an **objective** on the rotating nosepiece, typically 4x, 10x, 40x and 100x

**Total magnification = eyepiece × objective.** A 10x eyepiece with a 40x objective gives 400x.

Magnification alone is not enough. **Resolution** is the smallest distance between two points that you can still see as separate. For light microscopes it is about 0.2 µm, limited by the wavelength of light. That is why bacteria (1–5 µm) are visible but viruses (about 0.02–0.3 µm) generally are not. The 100x objective needs a drop of **immersion oil** between the lens and the slide to reach its best resolution.

Other parts you will use:

- **Stage** and stage clips (or a mechanical stage) to hold and move the slide
- **Coarse focus** knob for big movements, **fine focus** knob for sharpening
- **Light source**, **condenser** and **iris diaphragm** to control brightness and contrast

## Worked example: focusing routine

1. Start on the **lowest-power objective**. It has the widest field and the most room between lens and slide.
2. Watching from the side, raise the stage until the objective is close to the slide.
3. Looking through the eyepiece, focus by moving the stage **away** from the lens with the coarse knob. Moving away cannot crash the lens into the slide.
4. Centre the part you want, then switch to the next objective. Good microscopes are **parfocal**: the image stays nearly in focus, so use only the fine knob from now on.
5. Close the diaphragm a little if the specimen looks washed out; unstained cells often need lower light to show contrast.

You will notice that the image is **upside down and reversed**: move the slide left and the image moves right. A newsprint letter "e" makes this obvious.

## Worked example: measuring with the field of view

You can estimate size without special equipment.

1. At 4x, lay a clear ruler on the stage. Suppose 4.5 mm fits across the circle. The **field of view** is 4.5 mm = 4,500 µm.
2. Field of view shrinks in proportion to objective power. At 10x: 4,500 × (4 ÷ 10) = **1,800 µm**. At 40x: 4,500 × (4 ÷ 40) = **450 µm**.
3. At 10x you count about 6 onion cells across the field. Each cell is roughly 1,800 ÷ 6 = **300 µm** long.

Real labs use a calibrated **eyepiece graticule** and a **stage micrometer** for accurate measurements, but the logic is the same: know the size of what you are looking through, then compare.

Remember the units: 1 mm = 1,000 µm, and 1 µm = 1,000 nm.

## Care of the microscope

- Carry it with two hands: one on the arm, one under the base.
- Clean lenses only with lens paper, never tissue or your shirt.
- Wipe immersion oil off the 100x objective after use, and never let the 40x objective touch oil.
- Finish on the lowest objective with the stage lowered and the light off.

## Common mistakes

- **Starting on high power.** You will not find the specimen, and you may crack the slide.
- **Using the coarse knob at 40x or 100x.** It moves too far and can crash the lens.
- **Too much light.** Unstained cells disappear; close the diaphragm.
- **Reporting size without units or magnification.** Always say "about 300 µm at 100x total magnification".
- **Confusing magnification with resolution.** Making an image bigger does not reveal detail smaller than about 0.2 µm.

## Quick recap

- Total magnification = eyepiece × objective.
- Resolution of a light microscope is about 0.2 µm.
- Start low, focus away from the slide, then use only the fine knob at higher power.
- Field of view at a new objective = low-power field × (low objective ÷ new objective).
- Estimate size by dividing the field width by how many cells span it.

## Try it

Open the **Do** tab to focus a safe specimen and estimate cell size from the field of view.


Focus a slide specimen with a compound light microscope and estimate its size from the field of view.

Using a microscope

How to use a compound Microscope

BIOLOGY 10 - Basic Microscope Setup and Use

Tour the cell and its organelles, see how substances cross membranes, and learn to focus and measure a specimen with a light microscope.