Biochemists, biological technicians and medical laboratory technologists all work with cells, genes, microorganisms and human samples. This beginner course gives you the biology underneath that work. The first module tours the cell, explains how substances cross membranes by diffusion, osmosis and active transport, and walks through focusing and measuring a specimen with a light microscope. The second module follows information from DNA to RNA to protein, uses Punnett squares to predict inheritance (with a short fill-in-the-blank Python exercise), and shows how mutations change proteins. The third module compares bacteria, viruses and fungi, links blood and organ systems to common lab tests, and explains antigens and antibodies. It needs no prerequisites. It teaches knowledge, not hands-on lab competence: real lab and clinical work requires the training, supervision and qualifications your employer or program provides, and every activity here is safe to do at home or in a teaching lab with your instructor.

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.

Cells

## Why it matters

Most of modern biotechnology works on the path from DNA to protein. PCR copies DNA. RT-PCR (the basis of many viral tests) starts from RNA. Recombinant insulin is made by putting a human gene into cells so they translate it into protein. Biochemists study how proteins fold and work. To follow any of it, you need the **central dogma**: DNA makes RNA makes protein.

## The core idea: information flow

- **DNA** stores the information long-term in the nucleus.
- **Transcription** copies one gene into **messenger RNA (mRNA)**.
- **Translation** at the ribosome reads the mRNA and builds a chain of **amino acids**, which folds into a **protein**.

**DNA structure.** DNA is a double helix of two strands. Each strand is a chain of **nucleotides**, each with a sugar (deoxyribose), a phosphate and one of four **bases**: adenine (A), thymine (T), guanine (G) and cytosine (C). The strands are held together by base pairing: **A pairs with T, G pairs with C**. Because pairing is fixed, each strand is a template for the other, which is how DNA is copied before a cell divides.

**RNA** differs in three ways: it is usually single-stranded, its sugar is ribose, and it uses **uracil (U)** in place of thymine.

A **gene** is a stretch of DNA that codes for a functional product, usually a protein. Humans have roughly 20,000 protein-coding genes.

## Transcription

In the nucleus, the enzyme **RNA polymerase** binds to a **promoter** in front of the gene, unwinds the DNA and builds an mRNA strand complementary to the **template strand**. The mRNA ends up with the same sequence as the other DNA strand (the **coding strand**), except U replaces T.

In eukaryotes, the first transcript is processed before it leaves the nucleus: a cap and a poly-A tail are added, and non-coding **introns** are cut out (**splicing**), leaving the **exons** joined together.

## Translation and the genetic code

At the ribosome, the mRNA is read three bases at a time. Each triplet is a **codon**, and each codon stands for one amino acid or a stop signal.

- There are 4 × 4 × 4 = **64 codons** for **20 amino acids**, so most amino acids have several codons. The code is **redundant**.
- **AUG** codes for methionine and is the **start codon**.
- **UAA, UAG and UGA** are **stop codons**.
- **Transfer RNA (tRNA)** molecules carry amino acids. Each has an **anticodon** that pairs with a codon, so the right amino acid is added in the right order.

## Worked example: from gene to peptide

Coding strand of a tiny gene (5' to 3'):

```text
DNA coding strand:   ATG GGC TTT AAA TGA
DNA template strand: TAC CCG AAA TTT ACT
mRNA:                AUG GGC UUU AAA UGA
Amino acids:         Met Gly Phe Lys STOP
```

Step by step:

1. Write the mRNA by copying the coding strand and swapping T for U (or by pairing with the template strand: A→U, T→A, G→C, C→G).
2. Split the mRNA into codons from the start codon AUG.
3. Look each codon up in a codon table: AUG = Met, GGC = Gly, UUU = Phe, AAA = Lys, UGA = stop.
4. The peptide is **Met-Gly-Phe-Lys**. Translation stops at UGA, which adds no amino acid.

## From chain to working protein

The order of amino acids (the **primary structure**) determines how the chain folds into its 3D shape, and the shape determines what the protein does: an enzyme's active site, an antibody's binding pocket, a channel in the membrane. Heat, extreme pH or some chemicals can unfold (**denature**) a protein and destroy its function. That is why many lab enzymes and samples are kept cold.

## Common mistakes

- **Using T in RNA.** RNA uses U.
- **Reading codons from the wrong place.** Translation starts at AUG and reads in non-overlapping triplets; shifting by one base gives a completely different protein.
- **Thinking one gene always gives one protein.** Alternative splicing lets one gene make several related proteins.
- **Mixing up transcription and translation.** Transcription makes RNA (in the nucleus in eukaryotes); translation makes protein (at ribosomes).

## Quick recap

- DNA (A-T, G-C) stores information; RNA uses U instead of T.
- Transcription: RNA polymerase copies a gene into mRNA; introns are spliced out in eukaryotes.
- Translation: ribosomes read codons; tRNAs bring amino acids; AUG starts, UAA/UAG/UGA stop.
- 64 codons code for 20 amino acids, so the code is redundant.
- The amino acid sequence determines the fold, and the fold determines the function.


Describe how the information in DNA is transcribed into RNA and translated into protein.

DNA, genes, and proteins

Transcription and Translation: From DNA to Protein

From DNA to protein - 3D

## Why it matters

Inheritance patterns show up across lab careers. Clinical labs test for inherited conditions such as sickle cell disease and cystic fibrosis. Blood banks rely on the inheritance of ABO and Rh blood groups. Research labs breed model organisms (mice, fruit flies, plants) and must predict which offspring will carry a gene. The Punnett square is the simple tool behind all of these predictions.

## The core idea: alleles, genotypes, phenotypes

- A **gene** can come in different versions called **alleles**. For a gene with alleles **A** and **a**, a body cell has **two copies**: one from each parent.
- The pair of alleles is the **genotype**: **AA** and **aa** are **homozygous** (two of the same), **Aa** is **heterozygous**.
- The observable trait is the **phenotype**.
- A **dominant** allele (capital letter) shows its effect with one copy. A **recessive** allele (lower case) shows only when there are two copies.

Gregor Mendel's pea experiments gave two key rules:

1. **Segregation:** each parent passes on **one** of its two alleles, chosen at random, in each egg or sperm (gamete).
2. **Independent assortment:** alleles of different genes (on different chromosomes) are passed on independently of each other.

## Worked example 1: a monohybrid cross

Cystic fibrosis is recessive. Two parents are both carriers (**Aa**, where **a** is the CF allele). What are the chances for each child?

Write one parent's gametes across the top and the other's down the side, then fill each box with one allele from each:

| | **A** | **a** |
|---|---|---|
| **A** | AA | Aa |
| **a** | Aa | aa |

- Genotypes: **1 AA : 2 Aa : 1 aa**
- Phenotypes: **3 unaffected : 1 affected**
- Each child has a **1 in 4 (25%)** chance of having CF, a **1 in 2** chance of being a carrier, and a 1 in 4 chance of inheriting neither CF allele.

Note that this is a **probability for each child**. A family with four children could have zero, one or several affected children.

## Worked example 2: the test cross

A breeder has a mouse with the dominant phenotype. Is it **AA** or **Aa**? Cross it with a homozygous recessive (**aa**) mouse.

- If it is **AA**: every offspring is **Aa** and shows the dominant phenotype.
- If it is **Aa**: half the offspring are **Aa** and half are **aa** (recessive phenotype).

Seeing even one recessive offspring shows the parent is heterozygous. This is a standard tool in research animal facilities.

## Beyond simple dominance

Many traits do not follow the simple pattern:

- **Codominance:** both alleles show. ABO blood groups have alleles I^A, I^B and i. A person with I^A I^B is blood group **AB**, with both A and B antigens on their red cells.
- **Incomplete dominance:** the heterozygote is in between, like pink flowers from red × white snapdragons.
- **Sex-linked traits:** genes on the X chromosome, such as those for haemophilia A and red-green colour blindness, show up more often in males, who have one X.
- **Polygenic traits:** height and skin colour depend on many genes plus environment.

## Thinking like a programmer

A Punnett square is just "every allele from parent 1 combined with every allele from parent 2". That is two nested loops. In the Do activity, you finish a short Python function that does exactly that and counts the results. One detail matters: **Aa** and **aA** are the same genotype, so the code must write the dominant allele first before counting.

## Common mistakes

- **Putting both of a parent's alleles in one gamete.** Each gamete gets one allele.
- **Reading a ratio as a guarantee.** 3:1 is a probability per offspring, not an exact count in a small family.
- **Assuming dominant means common.** Some dominant alleles, such as the one for Huntington's disease, are rare.
- **Counting "aA" separately from "Aa".** They are the same heterozygous genotype.

## Quick recap

- Each parent passes one allele per gene to each offspring.
- A Punnett square combines every gamete from one parent with every gamete from the other.
- Aa × Aa gives 1 AA : 2 Aa : 1 aa, or 3 dominant : 1 recessive.
- A test cross with aa reveals whether a dominant-looking parent is AA or Aa.
- Codominance, incomplete dominance, sex linkage and polygenic traits extend the simple rules.

## Try it

Open the **Do** tab and complete a Python Punnett square counter.


Use Punnett squares to predict the genotypes and phenotypes of offspring from a one-gene cross.

Inheritance

Mendelian Genetics and Punnett Squares

Punnett Square Basics | Mendelian Genetic Crosses

## Why it matters

Genetic testing, cancer diagnostics, antibiotic resistance and vaccine updates all come down to **mutations**: changes in a DNA sequence. A molecular lab might sequence a tumour to find a mutation that guides treatment, or test bacteria for a resistance gene. To read such a result you need to know what kinds of mutation exist and what each does to the protein.

## The core idea

A **mutation** is any change in the DNA base sequence. Because the protein is built by reading the DNA in codons (three-base words), the effect depends on how the change affects those words.

Mutations arise from:

- **Copying errors** during DNA replication (rare, because DNA polymerase proofreads).
- **Mutagens:** UV light, tobacco smoke chemicals, some radiation.
- **Spontaneous chemical damage** to bases.

Cells have repair systems that fix most damage. What remains can be harmful, neutral or, occasionally, useful.

## Point mutations: one base changed

Take this stretch of mRNA and its protein:

```text
mRNA:     AUG  GAG  UGG  AAA
Protein:  Met  Glu  Trp  Lys
```

Change one base at a time:

| Type | Change | New codon | Effect |
|---|---|---|---|
| **Silent** | GAG → GA**A** | GAA = Glu | same amino acid; usually no effect (the code is redundant) |
| **Missense** | GAG → G**U**G | GUG = Val | one amino acid swapped; effect ranges from none to severe |
| **Nonsense** | UGG → UG**A** | UGA = stop | protein cut short; usually loses function |

**Worked example: sickle cell disease.** In the β-globin gene of haemoglobin, one A is replaced by T in the DNA. The mRNA codon changes from GAG to GUG, so the sixth amino acid changes from **glutamic acid to valine**. This single missense change makes haemoglobin stick together when oxygen is low, distorting red cells into a sickle shape. One base, one amino acid, a serious disease. Labs detect it with haemoglobin electrophoresis, HPLC or DNA tests.

## Insertions and deletions: frameshifts

Adding or removing bases that are **not a multiple of three** shifts the **reading frame**, so every codon after the change is different. An English analogy:

```text
Original:          THE CAT ATE THE RAT
Delete one "A":    THE CTA TET HER AT...
```

```text
mRNA:              AUG GAG UGG AAA
Delete first G:    AUG AGU GGA AA...
Protein:           Met Ser Gly ...   (every amino acid after the change is different)
```

Frameshifts usually produce a useless protein and often reach a premature stop codon. Deleting exactly three bases removes one amino acid without a frameshift. The most common cystic fibrosis variant, **ΔF508**, is a three-base deletion that removes one phenylalanine from the CFTR protein, causing it to misfold.

## Larger changes

Mutations can also affect chromosomes: duplications, deletions of whole segments, or **translocations** where pieces of two chromosomes swap. The "Philadelphia chromosome" in chronic myeloid leukaemia is a translocation between chromosomes 9 and 22 that creates a fusion gene; detecting it guides treatment.

## Where variation comes from

Mutation is the original source of all new alleles. Sexual reproduction then shuffles them:

- **Independent assortment** of chromosomes into gametes.
- **Crossing over**, where paired chromosomes swap segments during meiosis.
- **Random fertilisation**: any sperm with any egg.

Most variation between people is harmless. When a variant is common (found in more than about 1% of a population) it is often called a **polymorphism**. Clinical reports classify variants as pathogenic, likely pathogenic, of uncertain significance, likely benign or benign.

Mutations that occur in body cells (**somatic**) are not inherited but can cause cancer. Mutations in eggs or sperm (**germline**) can be passed to children.

## Mutation and microbes

Bacteria and viruses reproduce quickly, so useful mutations spread fast. A mutation that lets a bacterium survive an antibiotic is **selected** when that antibiotic is used, and the resistant strain takes over. RNA viruses such as influenza mutate quickly, which is one reason flu vaccines are updated each year.

## Common mistakes

- **Assuming every mutation is harmful.** Many are silent or neutral, and some are beneficial.
- **Thinking a missense change is always mild.** Sickle cell shows one amino acid can matter a lot.
- **Calling any deletion a frameshift.** Only deletions or insertions that are not multiples of three shift the frame.
- **Mixing up somatic and germline.** Only germline mutations are inherited.

## Quick recap

- A mutation is a change in DNA sequence; repair fixes most damage.
- Silent: same amino acid. Missense: different amino acid. Nonsense: early stop.
- Insertions or deletions that are not a multiple of three cause frameshifts.
- Sickle cell is a single missense change; CF ΔF508 is a three-base deletion.
- Mutation creates new alleles; meiosis and fertilisation shuffle them.


Explain how point mutations, insertions and deletions change a protein, and where genetic variation comes from.

Mutations and variation

Mutations (Updated)

Follow information from DNA to protein, predict inheritance with Punnett squares, and see how mutations change proteins.

Genetics and DNA

> **Awareness level only.** Do not try to grow microorganisms at home. In a lab, cultures and patient samples are handled at the biosafety level set by your institution, after training and under supervision.

## Why it matters

Microbiology labs identify the organism behind an infection so the right treatment can be chosen. Biotech labs grow bacteria and yeast to make insulin, enzymes and vaccines. Every lab protects its work from contamination. All of this starts with telling three big groups apart: **bacteria**, **viruses** and **fungi**.

## Bacteria

- **Prokaryotic cells**: no nucleus, a circular chromosome and often plasmids, ribosomes, a cell membrane and usually a **cell wall** made of peptidoglycan.
- Size about **1–5 µm**: visible with a light microscope.
- Shapes: **cocci** (spheres), **bacilli** (rods), **spirilla** (spirals).
- Reproduce by **binary fission**: one cell splits into two. Under good conditions some, like *E. coli*, can double about every 20 minutes.
- Most are harmless or helpful (gut bacteria, soil bacteria, bacteria used in yoghurt). A minority cause disease, such as *Streptococcus pyogenes* (strep throat) and *Mycobacterium tuberculosis*.

**The Gram stain** is one of the first tests on a bacterial sample. It sorts bacteria by cell wall:

- **Gram-positive** bacteria have a thick peptidoglycan wall that holds the purple crystal violet dye: they stain **purple**.
- **Gram-negative** bacteria have a thin wall plus an outer membrane, lose the purple dye and take up the red counterstain: they stain **pink/red**.

A report such as "Gram-positive cocci in clusters" (often *Staphylococcus*) gives the clinician an early clue hours or days before culture results.

**Treatment:** **antibiotics** target bacterial structures humans do not have, such as the peptidoglycan wall (penicillins) or bacterial ribosomes (tetracyclines).

## Viruses

- **Not cells.** A virus is genetic material (DNA or RNA) inside a protein coat called a **capsid**, sometimes wrapped in a lipid **envelope** taken from the host cell.
- Size about **20–300 nm**: too small for a light microscope; seen with an electron microscope.
- They have no ribosomes or metabolism, so they can reproduce **only inside a host cell**, by hijacking its machinery. Each virus infects particular cell types.
- Examples: influenza, SARS-CoV-2, HIV, hepatitis B.

**Treatment:** antibiotics **do not work** on viruses. Antiviral drugs target specific viral steps (for example, blocking a viral enzyme), and vaccines prepare the immune system in advance.

**Detection:** because viruses cannot be grown on plates, labs detect their genetic material with PCR or RT-PCR, or detect viral proteins (antigens) or the patient's antibodies against them (lesson 3).

## Fungi

- **Eukaryotic cells**: a nucleus and organelles, and a cell wall made of **chitin** (not peptidoglycan or cellulose).
- Two forms: single-celled **yeasts** (such as *Candida* and baker's yeast, *Saccharomyces*) and multicellular **moulds** made of threads called **hyphae** (such as *Aspergillus* and *Penicillium*).
- Reproduce by budding (yeasts) or by spores (moulds). Airborne mould spores are a common lab contaminant.
- Fungi gave us penicillin, are used in baking and brewing, and cause infections from athlete's foot to serious infections in people with weak immune systems.

**Treatment:** antifungal drugs, which often target **ergosterol**, the fungal version of cholesterol in their membranes.

## Side by side

| | Bacteria | Viruses | Fungi |
|---|---|---|---|
| Cell? | yes, prokaryotic | no | yes, eukaryotic |
| Size | 1–5 µm | 20–300 nm | yeasts ~3–10 µm; moulds larger |
| Genetic material | DNA (circular chromosome, plasmids) | DNA **or** RNA | DNA in a nucleus |
| Wall | peptidoglycan | none (capsid; some enveloped) | chitin |
| Reproduction | binary fission | only inside host cells | budding or spores |
| Treated with | antibiotics | antivirals, vaccines | antifungals |

## Worked example: reading a scenario

A patient has a sore throat. A rapid test detects a viral antigen. Should they get an antibiotic? No: antibiotics do not act on viruses, and unnecessary use drives **antibiotic resistance**. If instead the throat swab grows Gram-positive cocci in chains identified as *Streptococcus pyogenes*, an antibiotic such as penicillin is appropriate. The lab result changes the treatment.

## Common mistakes

- **Calling viruses bacteria or "germs" interchangeably.** They are fundamentally different, and treatment differs.
- **Expecting antibiotics to treat colds or flu.**
- **Forgetting fungi are eukaryotes.** That is why antifungal drugs can have more side effects: fungal cells resemble ours.
- **Assuming all microbes are harmful.** Most bacteria and fungi are harmless or useful.

## Quick recap

- Bacteria: prokaryotic cells, 1–5 µm, peptidoglycan wall, binary fission, antibiotics.
- Viruses: not cells, nanometre-sized, reproduce only in host cells, antivirals and vaccines.
- Fungi: eukaryotic, chitin wall, yeasts and moulds, antifungals.
- The Gram stain sorts bacteria into purple (Gram-positive) and pink (Gram-negative).


Compare bacteria, viruses and fungi by structure, reproduction and how labs identify and treat them.

Microorganisms

Bacteria (Updated)

Viruses (Updated)

## Why it matters

Clinical laboratories run a large share of the tests that inform medical decisions. A medical laboratory technologist does not diagnose patients, but they must understand what each test measures and why a result is plausible or not. Biochemists and biological technicians use the same physiology when they work with serum, plasma or tissue. This lesson connects the body's systems to the tests you will hear about most.

## Blood: the most tested tissue

Blood is about **55% plasma** and **45% cells** (the cell fraction is the **haematocrit**, typically around 40–50%).

- **Plasma** is mostly water carrying proteins (albumin, antibodies, clotting factors), glucose, electrolytes, hormones and waste such as urea.
- **Serum** is plasma with the clotting factors used up: what is left after blood clots in the tube. Many chemistry tests use serum; coagulation tests need plasma from a tube with an anticoagulant.

The cells:

| Cell | Job | Lab connection |
|---|---|---|
| **Red blood cells (erythrocytes)** | carry oxygen with haemoglobin; no nucleus; live about 120 days | RBC count, haemoglobin and haematocrit; low values suggest **anaemia** |
| **White blood cells (leukocytes)** | defend against infection (next lesson) | WBC count and **differential** (neutrophils, lymphocytes, monocytes, eosinophils, basophils) |
| **Platelets (thrombocytes)** | cell fragments that start clotting | platelet count; low counts raise bleeding risk |

These numbers come together in the **complete blood count (CBC)**, one of the most ordered tests anywhere. A raised neutrophil count often points to bacterial infection; a raised lymphocyte count is common in viral infections. Those are patterns for clinicians to interpret, not rules, but knowing them helps a technologist spot an implausible result.

## Organ systems and their tests

**Cardiovascular system.** The heart pumps blood through arteries, capillaries and veins. When heart muscle is damaged, cells release **troponin** into the blood, so a troponin test helps diagnose heart attacks. Cholesterol tests (a **lipid panel**) assess long-term risk.

**Kidneys (urinary system).** Kidneys filter the blood, remove waste and balance water and electrolytes. **Creatinine** and **urea (BUN)** rise when kidney filtration falls. Labs often report an **estimated glomerular filtration rate (eGFR)** calculated from creatinine. **Urinalysis** checks urine for protein, glucose, blood and cells.

**Liver (digestive system).** The liver processes nutrients and drugs and makes proteins such as albumin and clotting factors. **Liver function tests** include the enzymes ALT and AST (released when liver cells are damaged), bilirubin (raised in jaundice) and albumin.

**Endocrine system.** Glands release hormones into the blood. The pancreas makes **insulin**, which lowers blood glucose. **Glucose** and **HbA1c** (glucose stuck to haemoglobin, reflecting about the last three months, since red cells live about 120 days) are used to diagnose and monitor diabetes. The thyroid is checked with **TSH**.

**Electrolytes.** Sodium, potassium, chloride and bicarbonate keep nerves, muscles and fluid balance working. Remember the sodium-potassium pump from module 1: if a blood sample sits too long before separation, potassium leaks out of the cells and the result can be falsely high. Haemolysis (burst red cells) in the tube has the same effect.

## Worked example: a basic metabolic panel

A basic metabolic panel (BMP) bundles glucose, calcium, sodium, potassium, chloride, bicarbonate, urea and creatinine. Imagine a result with high potassium and a lab note: "specimen haemolysed". Because red cells contain far more potassium than plasma, the burst cells have released potassium into the sample. The technologist flags the result and requests a new sample rather than reporting a value that might send a clinician chasing a problem that is not there. Knowing the physiology turns a number into a judgement.

## Reference ranges

Every test result is compared with a **reference range**: the values found in most healthy people (often the middle 95%). Ranges differ between labs, methods, ages and sexes, so always use the range printed on the report. A value slightly outside the range is not automatically abnormal, and a value inside it does not rule out disease.

## The careers behind the tests

Running and verifying these tests is regulated work. In the US, medical laboratory scientists usually complete a NAACLS-accredited program with clinical rotations and earn ASCP Board of Certification (MLS) certification; some states, such as California, New York and Florida, also require a licence. This course teaches background knowledge only. Official sources: NAACLS, https://www.naacls.org and ASCP Board of Certification, https://www.ascp.org/boc (Checked on 2026-10-23.)

## Common mistakes

- **Using serum and plasma as if they were the same.** Serum has no clotting factors.
- **Reading a result without its reference range.**
- **Ignoring pre-analytical problems** such as haemolysis, delays or the wrong tube.
- **Confusing the CBC with chemistry panels.** The CBC counts cells; panels measure dissolved substances.

## Quick recap

- Blood is plasma plus red cells, white cells and platelets; the CBC counts them.
- Troponin for the heart, creatinine and eGFR for the kidneys, ALT/AST and bilirubin for the liver, glucose and HbA1c for diabetes.
- Electrolytes reflect fluid balance; haemolysis can falsely raise potassium.
- Always interpret results against the lab's own reference range.


Relate blood components and major organ systems to the common lab tests that check them.

Human physiology essentials

Blood, Part 1 - True Blood: Crash Course Anatomy & Physiology #29

The Composition and Function of Blood

## Why it matters

The immune system is the reason many lab tests work. Pregnancy tests, COVID-19 rapid tests, blood typing, allergy tests and ELISA assays all use **antibodies** that bind specific targets. Biochemists engineer antibodies as drugs; medical laboratory technologists use them every day in blood banks and immunology sections. To understand those tests, you need to know what antigens and antibodies are.

## Two lines of defence

**Innate immunity** is fast (minutes to hours) and general. It includes:

- barriers: skin, mucus, stomach acid
- **phagocytes** such as **neutrophils** and **macrophages** that engulf microbes (phagocytosis, from module 1)
- **inflammation**: redness, heat, swelling, which brings more cells to the site
- fever and complement proteins that punch holes in bacteria

**Adaptive immunity** is slower the first time (days) but **specific**, and it **remembers**. It relies on **lymphocytes**:

- **B cells** make antibodies.
- **T cells**: **helper T cells** coordinate the response; **cytotoxic T cells** kill infected or abnormal cells.

## Antigens and antibodies

An **antigen** is any molecule the immune system can recognise, usually a protein or sugar on a microbe, a cell or a toxin. The small region an antibody actually binds is the **epitope**.

An **antibody** (immunoglobulin, Ig) is a Y-shaped protein made by B cells (as plasma cells). It has:

- two identical **arms** with **variable regions** at the tips that bind one specific epitope, like a lock and key
- a **stem** (constant region) that signals to other immune cells

Antibodies **neutralise** toxins and viruses, **clump** (agglutinate) microbes together and **tag** them for phagocytes.

The main classes:

| Class | Notes |
|---|---|
| **IgM** | first antibody made in a new infection; large five-unit form |
| **IgG** | most common in blood; made later and in memory responses; crosses the placenta |
| **IgA** | in mucus, saliva, tears and breast milk |
| **IgE** | involved in allergies and parasites |
| **IgD** | on the surface of B cells |

A positive **IgM** suggests a recent infection; **IgG** alone often suggests past infection or vaccination. Clinicians interpret these patterns; the lab must report them accurately.

## Memory and vaccines

After an infection, some B and T cells become long-lived **memory cells**. The next time the same antigen appears, the **secondary response** is faster, larger and mostly IgG. Vaccines use this: they present a harmless form of an antigen (an inactivated virus, a protein subunit or mRNA that instructs your cells to make a protein) so memory forms without the disease.

## Worked example 1: ABO blood typing

Red blood cells carry antigens A, B, both or neither. Plasma contains antibodies against the antigens a person **does not** have.

| Blood group | Antigens on red cells | Antibodies in plasma |
|---|---|---|
| A | A | anti-B |
| B | B | anti-A |
| AB | A and B | none |
| O | none | anti-A and anti-B |

In forward typing, the lab mixes a patient's red cells with anti-A and anti-B reagents. **Agglutination** (clumping) with anti-A only means group A. Clumping with both means AB; with neither means O. This is why a transfusion of the wrong group is dangerous: the recipient's antibodies attack the donor's cells. Blood bank work is highly regulated and always done under trained supervision with confirmatory checks.

## Worked example 2: a lateral flow test

A home rapid antigen test is an immunoassay on a strip:

1. The sample flows over **labelled antibodies** (attached to coloured particles) that bind the viral antigen.
2. At the **test line**, fixed antibodies capture the antigen-antibody complex, and the colour builds up into a visible line.
3. At the **control line**, other fixed antibodies capture the labelled antibodies whether or not antigen is present. No control line means the test is invalid.

Laboratory **ELISA** tests use the same idea in plastic wells, with an enzyme that produces a colour change measured by a plate reader, which gives a number rather than a yes/no line.

## Common mistakes

- **Mixing up antigen and antibody.** The antigen is the target; the antibody is the protein that binds it.
- **Thinking group O has no antibodies.** Group O has no A or B antigens but has both anti-A and anti-B.
- **Ignoring the control line** on a lateral flow test.
- **Assuming the immune system only fights microbes.** It also causes allergies, transplant rejection and autoimmune disease.

## Quick recap

- Innate immunity is fast and general; adaptive immunity is specific and has memory.
- B cells make antibodies; T cells help or kill.
- Antibodies bind specific epitopes on antigens and neutralise, clump or tag them.
- IgM comes first; IgG is the main long-term and memory antibody.
- Blood typing, lateral flow tests and ELISA all use antigen-antibody binding.


Explain how antigens and antibodies work and how labs use them in blood typing and immunoassays.

The immune system

Immune System, Part 1: Crash Course Anatomy & Physiology #45

Immune System, Part 2: Crash Course Anatomy & Physiology #46

Compare bacteria, viruses and fungi, connect blood and organ systems to lab tests, and understand antigens and antibodies.

Biology Fundamentals

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Cells

Genetics and DNA

Organisms and Systems

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