Domains, Kingdoms and DNA

A mushroom pops up on a dead log after rain. It does not walk, swim or fly away. For a long time, many scientists grouped mushrooms with plants. Today they sit in their own kingdom, and DNA shows they are closer to you than to an oak tree. How did that happen?

Explore: sort living things by evidence

In the model you see six cards: a mushroom, an oak, a deer, a paramecium, a bacterium and an archaeon. A slider adds evidence one kind at a time: what your eyes see, then a light microscope, then cell chemistry, then DNA. The cards move into new groups, and a bar shows how alike one protein is for the pairs the lesson measured.

Evidence available: What eyes see

What eyes see Light microscope Cell chemistry DNA

Organism A Mushroom Oak Deer Paramecium Bacterium Archaeon Organism B Mushroom Oak Deer Paramecium Bacterium Archaeon Reset

Protein match (one protein) for the pair you picked

Made up for this sketch: only six organisms; boxes, not branches; the order of the four kinds of evidence; the mushroom, deer and oak stand in for groups the table measured with other organisms; bar values are that table’s means, rounded.

Rule to keep: the more alike two organisms’ DNA sequences are, the more recent their common ancestor, and new evidence can change the groups.

Try this.

1. Set the slider to “what eyes see.” Predict which card the mushroom will sit with. Then check.
2. Predict what happens to the bacterium and the archaeon when you add the microscope, and then when you add cell chemistry. Test each step.
3. Pick the mushroom and the deer, then the mushroom and the oak. Predict which pair has the taller protein bar.

Explain: four clues sort life into domains and kingdoms

You met the levels of classification, from domain down to species, in that lesson. Here you see how scientists choose an organism’s domain and kingdom. They ask four questions:

• Do its cells have a nucleus? A nucleus is the part of a cell that holds its DNA.
• Which cell parts does it have? A cell wall is a stiff layer outside the cell membrane. A chloroplast is a green part where a cell makes sugar (glucose) using light.
• Does it have one cell or many?
• Does it make its own food, or take food in?

The first question splits life into cells with a nucleus and cells without one. Genes and chemistry then split the cells without a nucleus into two domains, so life has three domains. Bacteria is a domain of tiny, mostly single-celled organisms with no nucleus. Archaea is a second domain of mostly single-celled organisms with no nucleus. Eukarya is the domain of all organisms whose cells have a nucleus.

Bacteria and Archaea look alike under a light microscope. But their chemistry and their genes show they are very different from each other, and from Eukarya.

Many US textbooks then use six kingdoms. Bacteria and Archaea each get one. The other four are inside Eukarya.

Kingdom	Nucleus?	Cell wall?	Chloroplasts?	Cells	Food
Bacteria	No	Most have one	No	Mostly one	Some make it, some take it in
Archaea	No	Most have one	No	Mostly one	Some make it, some take it in
Protists	Yes	Some	Some	Most one, some many	Some make it, some take it in
Fungi	Yes	Yes	No	Most many; yeast one	Take it in
Plants	Yes	Yes	Yes, in green parts	Many	Make it
Animals	Yes	No	No	Many	Take it in

A protist is an organism with a nucleus that is not a plant, animal or fungus, such as a paramecium. A fungus is an organism with a nucleus and a cell wall but no chloroplasts, which takes in food from what it grows on.

Explain: new tools bring new evidence

The groups have changed many times, each time after a new kind of evidence.

Year	Scientist	Groups	New evidence behind it
1735	Linnaeus	2 kingdoms of living things	Body parts seen by eye
1866	Haeckel	3 kingdoms	Tiny living things that were neither plant nor animal
1938	Copeland	4 kingdoms	Cells with no nucleus put in their own kingdom
1969	Whittaker	5 kingdoms	Fungi separated by how they get food
1977	Woese and Fox	3 main lines of life	Comparing a molecule all cells have (ribosomal RNA)
1990	Woese, Kandler and Wheelis	3 domains	Molecule comparisons; a new level above kingdom

Mushrooms show how this works. Mushrooms stay in one place, like plants. But a closer look showed that fungal cells have no chloroplasts, so fungi cannot make sugar from light. Instead, a fungus releases digesting substances outside its cells and takes in the small pieces. A mushroom on a log feeds on the dead wood. Other fungi feed on living hosts or trade food with living plants.

Then came DNA. A DNA sequence is the order of the chemical letters in a stretch of DNA. Each protein is built from a gene’s instructions, so comparing proteins is another way to compare genes. You will read about DNA in that lesson.

The more alike two organisms’ DNA sequences are, the more closely related they are. A common ancestor is an organism that two groups both descend from. These comparisons put fungi closer to animals than to plants. That does not make a mushroom an animal. It means fungi and animals share a more recent common ancestor than either shares with plants.

Elaborate: compare one protein in five organisms

The table compares one protein, called EF-1 alpha, which all five organisms make. A computer lined up the protein from two organisms at a time and counted the positions that matched.

Pair compared	Kind of pair	Matching positions (out of positions compared)	Match (%)
Human and baker’s yeast	Animal and fungus	371 of 460	80.7
Human and bread mold	Animal and fungus	387 of 461	83.9
Baker’s yeast and thale cress	Fungus and plant	339 of 461	73.5
Baker’s yeast and wheat	Fungus and plant	336 of 457	73.5
Bread mold and thale cress	Fungus and plant	342 of 462	74.0
Bread mold and wheat	Fungus and plant	345 of 458	75.3
Baker’s yeast and bread mold	Fungus and fungus	394 of 460	85.7
Thale cress and wheat	Plant and plant	425 of 446	95.3

Source: protein records from the NCBI Protein database, compared with NCBI’s BLAST program on 23 October 2026 for this course. Thale cress is a small weed used in plant research. These percents are for one protein, not for all of the DNA.

1. Find the mean match for the two animal-and-fungus pairs. Then find the mean for the four fungus-and-plant pairs.
2. Which is higher, and by about how many percentage points?
3. Which pair matches best of all? Why does that make sense?

Design problem

A fungus takes in food. Does baker’s yeast, a single-celled fungus, need sugar to stay active? Plan a test. Active yeast gives off a gas, carbon dioxide, which you can collect in a balloon.

One way to do it

• Question: Does yeast give off more gas when it has sugar to take in?
• Independent variable: sugar added (0 grams or 10 grams).
• Dependent variable: the distance around the balloon, in centimetres, after 30 minutes.
• Constants: 7 grams of yeast, 100 millilitres of warm tap water, the same size bottle and balloon, the same room.
• Control: the bottle with yeast and water but no sugar.
• Trials: three bottles of each kind; find the mean of each.
• What results mean: larger balloons with sugar show the yeast takes in sugar and breaks it down. Similar balloons would mean sugar made no difference here.
• Safety: use warm tap water, never a flame or stove. Wear goggles, do not taste anything, and wash your hands.

Evaluate: check your thinking

A mushroom stays in one place, but its cells have a nucleus, a cell wall and no chloroplasts, and it takes in food. Those clues put fungi in their own kingdom. DNA and protein comparisons then showed that fungi share a more recent common ancestor with animals than with plants.

Science practices you used: sorting organisms with evidence, reading a data table and finding a mean, making a claim with evidence and naming a limit, and planning a fair test with a control and repeated trials.