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

Biology Fundamentals

> **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.