TAXONOMY

A Comprehensive Study Guide

Topics Covered:

ˆ What is Taxonomy?
ˆ Taxonomic Ranks & Classification
ˆ Binomial Nomenclature
ˆ Biological Species Concept
ˆ The Three Domains of Life
ˆ Viruses
ˆ Kingdom Protista
ˆ Examination Questions

SMNS Biology Department

Biology Taxonomy Notes

What is Taxonomy?

Taxonomy is a branch of science that deals with the description, identification,

nomenclature, and classification of organisms. It aims to arrange organisms into
a hierarchical system called taxonomic ranks, based on shared characteristics or
evolutionary (phylogenetic) relationships.

A specialist in this field is called a taxonomist. The most famous taxonomist is

the Swedish botanist Carl Linnaeus (1707–1778), who is regarded as the Father of
Taxonomy. His major contributions include:

ˆ The Linnaean classification system — organising organisms into taxa (groups)

ˆ The system of binomial nomenclature — giving every species a two-part scientific

name

ˆ Developing his classification system in 1735

Remember!
Organisms can also be classified into clades in phylogenetic taxonomy — a clade
is a group of organisms that share a common ancestor and all its descendants.

Taxonomic Ranks
The classification system arranges organisms from the most general to the most specific.
The full hierarchy from broadest to narrowest is:

Domain → Kingdom → Phylum →

Class → Order → Family → Genus
→ Species

Remember!
Capitalisation Rule: All taxonomic ranks are written with a capital letter except
for species. Only Genus and species are italicised. For example: Homo sapiens
(not Homo Sapiens).

Domain
Domain is the highest and most general rank. Linnaeus did NOT invent this rank —
it was introduced in 1990, more than 250 years after his classification system. There are
three domains:

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Biology Taxonomy Notes

Domain Description
Bacteria Single-celled prokaryotes with unique cell walls
and rRNA
Archaea Single-celled prokaryotes; similar to bacteria but
genetically distinct
Eukaryota All organisms with a membrane-bound nucleus
(everything else)

Remember!
Eukaryota are more closely related to Archaea than to Bacteria. Also note: “bacte-
ria” (lowercase) refers to the organisms generally, while “Bacteria” (capital) refers
to the domain.

Kingdom
Life was traditionally separated into five or six kingdoms: Animals, Plants, Fungi,
Protists, Archaea, and Bacteria. With advances in genetics, we now know some kingdoms
(especially Protists) may need to be split further.

Phylum (plural: Phyla)

Phylum splits kingdoms into broad groups. Examples:

ˆ Arthropoda — includes insects, spiders, crustaceans

ˆ Chordata — includes all vertebrate animals

ˆ Invertebrates are spread across many different phyla

Class
Class divides phyla further. Examples from Chordata: Mammalia (mammals), Reptilia
(reptiles), Amphibia (amphibians). From Arthropoda: Insecta (insects), Arachnida (spi-
ders, mites, scorpions).

Order
Order is more specific than class. Examples:

ˆ Lepidoptera — butterflies and moths (still used from Linnaeus’s system)

ˆ Primates — humans, apes, monkeys

ˆ Cetacea — whales, dolphins, porpoises

ˆ Carnivora — large carnivores and omnivores (bears, dogs, cats, etc.)

ˆ Chiroptera — bats

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Biology Taxonomy Notes

Family
Family is more specific than order. Examples from Carnivora:

ˆ Canidae — dogs, wolves, foxes

ˆ Felidae — cats

ˆ Mephitidae — skunks

ˆ Ursidae — bears

There are 12 families total in the order Carnivora.

Genus (plural: Genera)

Genus is the first part of a scientific name. It is capitalised and italicised. For example,
in Homo sapiens, Homo is the genus. Related extinct species in the same genus include
Homo erectus and Homo neanderthalensis (Neanderthals).

Species
Species is the most specific major rank. The species name is always lowercase and
italicised. It is the only rank that is NOT capitalised. Key points:

ˆ There are an estimated 8.7 million species on Earth, most yet to be discovered

ˆ The same species name can be shared by different organisms (e.g., Ursus americanus
= American black bear; Bufo americanus = American toad)

ˆ After first use, the genus is abbreviated: Homo sapiens becomes H. sapiens

Human Classification Example

Rank Classification
Domain Eukaryota
Kingdom Animalia
Phylum Chordata
Class Mammalia
Order Primates
Family Hominidae
Genus Homo
Species Homo sapiens

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Biology Taxonomy Notes

Binomial Nomenclature

Binomial nomenclature is a two-part naming system for species, often based on

Latin or Greek. Every species gets a unique scientific name consisting of:

1. Generic name (Genus) — capitalised

2. Specific epithet (Species) — lowercase

The entire name is italicised (or underlined if handwritten).

Examples:

ˆ Homo sapiens — humans

ˆ Yucca filamentosa — a type of plant (abbreviated: Y. filamentosa)

ˆ Homo erectus — an extinct human ancestor

Why do we name organisms?

ˆ A name acts as a means of reference

ˆ It aids communication in science across different languages

ˆ It avoids the use of long descriptive phrases when referring to an organism

Remember!
Latin is used even though it is a dead language because it does not change over
time, making scientific names stable and universal.

Biological Species Concept (BSC)

The Biological Species Concept defines a species as a group of populations whose

members are capable of interbreeding successfully and are reproductively iso-
lated from other groups.

This concept was made influential in the late 19th and early 20th centuries. Ernst
Mayr (1942) defined it as: ”species are groups of interbreeding natural populations that
are reproductively isolated from other such groups.”
Key ideas:

ˆ Sexual reproduction maintains genetic uniformity within a species through a shared

gene pool

ˆ Isolating mechanisms prevent gene flow between different species, causing genetic
divergence

ˆ Mayr’s definition excludes artificial or captive matings

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Biology Taxonomy Notes

Problems Applying the BSC

1. Cloning / Asexual Reproduction
Many organisms reproduce asexually (bacteria, some lizards, salamanders, plants like
strawberries, Bermuda grass, dandelions, redwoods), so the BSC cannot apply to them.

2. Variation and Ring Species

Some species interbreed in narrow zones of overlap. For example, the Oregon Junco (Junco
oreganus), Gray-headed Junco, Slate-coloured Junco, and White-winged Junco all look
like separate species but interbreed where their ranges overlap, forcing ornithologists to
classify them all under one species, the Dark-eyed Junco (J. hyemalis).

3. Hybridisation
Hybrids are individuals with genes from two different species. They live in hybrid
zones where species overlap. Hybrids are usually less fertile than either parent species.
Parent populations remain largely genetically distinct despite some gene exchange.

Remember!
The BSC cannot be used to classify bacteria or other asexually reproducing organ-
isms because it requires organisms to interbreed and produce viable fertile offspring.

The Three Domains of Life

Domain Archaea
ˆ Single-celled prokaryotes — no membrane-bound nucleus

ˆ Genes are similar to both bacteria and eukaryotes

ˆ Originally mistaken for bacteria due to similar appearance

ˆ Reproduce by binary fission, have one circular chromosome, use flagella for move-
ment

ˆ Differ from bacteria in cell wall composition and from both bacteria and eukary-
otes in membrane composition and rRNA type

ˆ Often extremophiles (live in extreme conditions): hydrothermal vents, acidic

springs, Arctic ice

Three main phyla of Archaea:

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Biology Taxonomy Notes

Phylum Description
Crenarchaeota Includes hyperthermophiles (extreme heat) and
thermoacidophiles (hot & acidic environments)
Euryarchaeota Includes methanogens — produce methane as a
metabolic byproduct; require oxygen-free envi-
ronments
Korarchaeota Little known; found in hot springs, hydrother-
mal vents, obsidian pools

Domain Bacteria
ˆ Classified under the Bacteria domain

ˆ Some are pathogenic (disease-causing); many are beneficial (human microbiota, di-
gestion, nutrient recycling)

ˆ Bacteria on skin prevent pathogenic colonisation and activate the immune system

ˆ Unique cell wall composition and rRNA type

Five main phyla of Bacteria:

Phylum Description
Proteobacteria Largest group; includes E. coli, Salmonella, Heli-
cobacter pylori, Vibrio
Cyanobacteria Capable of photosynthesis; also called blue-green
algae
Firmicutes Gram-positive; includes Clostridium, Bacillus, my-
coplasmas
Chlamydiae Parasitic; reproduce inside host cells; includes
Chlamydia trachomatis (STD) and Chlamydophila
pneumoniae (pneumonia)
Spirochetes Corkscrew-shaped; unique twisting motion; in-
cludes Borrelia burgdorferi (Lyme disease) and
Treponema pallidum (syphilis)

Domain Eukarya
ˆ All organisms with a membrane-bound nucleus

ˆ Subdivided into kingdoms: Protista, Fungi, Plantae, Animalia

ˆ Distinct rRNA from bacteria and archaea

ˆ Plant and fungal cell walls differ in composition from bacteria

ˆ Generally resistant to antibacterial antibiotics

ˆ Examples: algae, amoeba, fungi, ferns, mosses, flowering plants, sponges, insects,
mammals

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Biology Taxonomy Notes

Viruses

Viruses are ultra-microscopic, non-cellular particles composed of a nucleic acid core

(DNA or RNA) surrounded by a protein coat called a capsid.

Characteristics of Viruses
1. Non-cellular and very simple in structure (nucleic acid + capsid)

2. A unit of virus is called a virus particle, NOT a virus cell

3. Lack enzymatic and biosynthetic machinery — can only replicate inside living
host cells

4. Ultra-microscopic — visible only under an electron microscope

5. Do not increase in size

6. Can pass through filters that bacteria cannot

7. A virus contains either DNA or RNA, never both

Bacteriophages
Viruses that infect bacteria are called bacteriophages (or phages). The name comes
from Greek meaning “to eat bacteria.” They were first described in 1915 by Twort and
d’Herelle.
Structural components of bacteriophages:

Component Function
Capsid (ProteinProtects nucleic acid from destruction by
Coat) DNase
Nucleic Acid Core Contains the phage genome; carries genetic
information for replication
Spiral Protein Retracts to allow nucleic acid to pass into
Sheath host cell cytoplasm
End Plate & Tail Attach the phage to receptor sites on the host
Fibres cell wall

Viral Infection — Five Sequential Steps

1. Attachment — Tail fibres bind to specific receptor sites on the host cell wall

2. Injection (Penetration) — Protein sheath retracts; enzyme (early muramidase)

perforates cell wall; nucleic acid enters the host cell. The empty protein shell
(“protein ghost”) remains outside

3. Synthesis — Phage genome hijacks the host cell’s machinery to produce new phage
components

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Biology Taxonomy Notes

4. Assembly — New phage components are assembled into complete, mature phage
particles
5. Release — Late muramidase lyses the cell wall; infectious phage particles are re-
leased to infect new cells

Kingdom Protista

All single-celled eukaryotic organisms are placed in Kingdom Protista. The term
was first used by Ernst Haeckel in 1886. Protists bridge the gap between plants,
animals, and fungi. The first protists evolved approximately 1.7 billion years ago.

General Characteristics
ˆ Simple eukaryotic organisms with a membrane-bound nucleus

ˆ Mostly unicellular; some colonial or multicellular (e.g., algae)

ˆ Primarily aquatic; some in moist soil or inside other organisms

ˆ Have mitochondria (cellular respiration); some have chloroplasts (photosynthesis)

ˆ Move using flagella or cilia

ˆ Reproduce both sexually and asexually; some form cysts in adverse conditions

ˆ Can be heterotrophic or autotrophic

ˆ Include at least 16 phyla

ˆ Some (e.g., algae) are primary producers in aquatic ecosystems

ˆ Some cause serious human diseases (malaria, sleeping sickness)

Classification of Kingdom Protista

Protista are divided into two main groups:

A. Animal-like Protists — Protozoans

Protozoans are heterotrophic (cannot make their own food) and motile (can move).
They are classified by how they move:

Phylum Movement Example

Sarcodina Pseudopodia Amoeba, Foraminiferans
Mastigophora Flagella Trypanosoma gambiense (sleep-
ing sickness)
Ciliophora Cilia Paramecium (slipper animalcule)
Sporozoa Non-motile; Plasmodium (malaria)
form spores

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Biology Taxonomy Notes

B. Plant-like Protists — Algae

Algae have chlorophyll and carry out photosynthesis. They are believed to be the major
oxygen suppliers on Earth and are the primary food producers for aquatic ecosystems.

Phylum Common Name Key Features / Examples

Chlorophyta Green Algae Freshwater; cellulose cell walls;
Spirogyra
Rhodophyta Red Algae Marine; source of agar and car-
rageenan; Nori, Gelidium
Phaeophyta Brown Algae Multicellular; kelps; source of
algin; Sargassum
Chrysophyta Golden Algae Diatoms most abundant; silica
shells; “diatomaceous earth”
Pyrrophyta Fire Algae Dinoflagellates; biolumi-
nescent; cause red tide;
Gonyaulax

C. Fungus-like Protists — Slime Moulds

Slime moulds are saprophytic (feed on decaying matter), live in moist soil and decaying
plants, are normally single-celled, but form multicellular aggregations called plas-
modium under favourable conditions. In unfavourable conditions, they produce spore-
bearing fruiting bodies.

Economic Importance of Protists

ˆ Food — Kelps and some algae are edible

ˆ Commercial products — Algin, agar, carrageenan, antiseptics

ˆ Aquatic ecosystem — Primary producers; support food chains and provide oxy-
gen

ˆ Medicine — Sodium laminaria sulphate, Fucoidin, Heparin (blood coagulants);

Lyngbya (anti-cancer)

ˆ Minerals — Kelps are rich in sodium, potassium, iodine

ˆ Biological research — Chlorella used in photosynthesis studies

ˆ Pathogens — Cause malaria, sleeping sickness, late blight of potatoes

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Biology Taxonomy Notes

Examination Questions

Instructions: Answer all questions. Write neatly and show your reasoning where
required.

Part A: Multiple Choice Questions

Circle the letter of the best answer for each question.

1. Who is known as the Father of Taxonomy?

A. Charles Darwin C. Carl Linnaeus

B. Ernst Mayr D. Ernst Haeckel

2. Which taxonomic rank is the BROADEST (most general)?

A. Kingdom C. Domain
B. Phylum D. Class

3. Which of the following is correctly written in binomial nomenclature?

A. homo Sapiens C. Homo sapiens

B. Homo Sapiens D. homo sapiens

4. What is the protein coat of a virus called?

A. Capsule C. Nucleoid
B. Capsid D. Cell wall

5. The term “Domain” was first used in which year?

A. 1735 C. 1942
B. 1886 D. 1990

6. Which domain contains organisms with a membrane-bound nucleus?

A. Bacteria C. Eukaryota
B. Archaea D. Protista

7. What is the scientific name for humans?

A. Homo erectus C. Homo neanderthalensis

B. Homo sapiens D. Homo habilis

8. Which phylum includes all vertebrate animals?

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Biology Taxonomy Notes

A. Arthropoda C. Mollusca
B. Chordata D. Annelida

9. Which of the following organisms is a member of Phylum Sporozoa?

A. Paramecium C. Plasmodium
B. Amoeba D. Trypanosoma

10. What type of nucleic acid can a single virus contain?

A. DNA only C. Both DNA and RNA

B. RNA only D. Either DNA or RNA, but not both

11. Which bacterial phylum is capable of photosynthesis?

A. Firmicutes C. Cyanobacteria
B. Proteobacteria D. Spirochetes

12. What causes Lyme disease?

A. Treponema pallidum C. E. coli

B. Borrelia burgdorferi D. Chlamydia trachomatis

13. The Biological Species Concept was formulated by which scientist?

A. Carl Linnaeus C. Ernst Mayr

B. Charles Darwin D. Ernst Haeckel

14. Which Archaean phylum includes methanogens?

A. Crenarchaeota C. Euryarchaeota
B. Korarchaeota D. Proteobacteria

15. In the viral infection process, what is the “protein ghost”?

A. The newly formed virus particles re- C. The host cell that has been de-
leased from the cell stroyed by the virus
B. The empty protein shell remaining
attached to the cell wall after injec- D. The nucleic acid core left inside the
tion host cell

16. Which algae are used as a source of agar?

A. Green algae (Chlorophyta) C. Brown algae (Phaeophyta)

B. Red algae (Rhodophyta) D. Golden algae (Chrysophyta)

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Biology Taxonomy Notes

17. Which taxonomic ranks are italicised?

A. Domain and Kingdom C. Genus and Species

B. Family and Genus D. Order and Family

18. The estimated number of species on Earth is approximately:

A. 1.7 million C. 16 million

B. 8.7 million D. 87 million

19. Trypanosoma gambiense causes which disease?

A. Malaria C. Sleeping sickness

B. Cholera D. Typhoid

20. Which of the following is NOT a characteristic of viruses?

A. They are non-cellular C. They are ultra-microscopic

B. They can replicate independently D. They contain nucleic acid

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Biology Taxonomy Notes

Part B: Cloze (Fill in the Blank) Questions

Fill in each blank with the correct word or phrase.

1. Taxonomy is a branch of science that deals with the description, ,

nomenclature and of organisms.

2. The person who specialises in taxonomy is called a .

3. Carl Linnaeus is known as the of Taxonomy and developed

his classification system in the year .

4. The three domains of life are , , and .

5. In binomial nomenclature, the first part of the scientific name is the

name and the second part is the name.

6. The scientific name for humans is , where Homo is the

and sapiens is the .

7. All taxonomic ranks are capitalised except for .

8. Only and are the taxonomic ranks that are italicised.

9. The protein coat of a virus is called the .

10. A virus that infects bacteria is called a .

11. After a phage injects its nucleic acid into the host cell, the empty protein shell that
remains is called the .

12. The Biological Species Concept states that a species is a group of populations ca-
pable of and are isolated from other groups.

13. Ernst Mayr proposed the Biological Species Concept in the year .

14. Kingdom Protista was first named by in the year .

15. Archaea differ from bacteria in composition and differ from both
bacteria and eukaryotes in composition and rRNA type.

16. Plasmodium, found in Phylum Sporozoa, causes in humans.

17. Brown algae belong to Phylum , while red algae belong to Phylum
.

18. Diatomaceous earth is formed from the shells of fossil , which are made
of .

19. Viruses can only be seen using an microscope.

20. Archaea that live in extremely hot and acidic environments are called .

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Biology Taxonomy Notes

Part C: Short Answer Questions

Answer each question in 2–5 sentences.

1. What is taxonomy and why is it important in biology?

2. Explain the difference between the terms “bacteria” (lowercase) and “Bacteria”
(uppercase) as used in taxonomy.

3. List and briefly describe the three domains of life.

4. What is binomial nomenclature? Give two examples of scientific names and explain
each part.

5. Describe two major contributions of Carl Linnaeus to taxonomy.

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Biology Taxonomy Notes

6. What are the five sequential steps in viral (phage) infection?

7. Explain why the Biological Species Concept cannot be applied to bacteria.

8. Compare and contrast archaea and bacteria. Give at least three similarities and
three differences.

9. What are protozoans? Name the four phyla of protozoans and state how each moves.

10. Describe three ways in which protists are economically important.

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Biology Taxonomy Notes

11. What is a hybrid zone? Why are hybrid zones considered a problem for the Biological
Species Concept?

12. Explain what diatomaceous earth is and give two of its practical uses.

13. Name three structural components of a bacteriophage and state the function of each.

14. Why are slime moulds classified as protists rather than fungi? Describe their be-
haviour under both favourable and unfavourable conditions.

15. What is the significance of the Dark-eyed Junco example in demonstrating the
limitations of the Biological Species Concept?

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Biology Taxonomy Notes

Part D: Essay Questions

Answer each question in well-organised, detailed paragraphs. Use examples to support
your answers.

1. [15 marks] Discuss the system of taxonomic classification in detail. In your answer,
describe all eight major taxonomic ranks from the broadest to the most specific, ex-
plain the rules of binomial nomenclature, and use the classification of Homo sapiens
as a worked example throughout your discussion.

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Biology Taxonomy Notes

2. [12 marks] Evaluate the Biological Species Concept. In your essay: (a) define and
explain the concept, including the role of reproductive isolation; (b) describe three
specific problems scientists face when trying to apply it to living organisms; and (c)
conclude by stating whether you think the BSC is still a useful concept despite its
limitations.

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Biology Taxonomy Notes

3. [15 marks] Write a comprehensive account of viruses. Your essay should cover: (a)
the definition and key characteristics of viruses; (b) the structure of a bacteriophage
and the function of each structural component; and (c) a step-by-step description
of how a bacteriophage infects a host bacterial cell, from attachment through to
release.

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Biology Taxonomy Notes

4. [12 marks] Describe Kingdom Protista in detail. In your essay, explain: (a) the
general characteristics of protists; (b) the classification of protists into animal-like
(protozoans) and plant-like (algae) groups, with examples of each phylum; and (c)
the economic importance of protists to humans and ecosystems.

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Biology Taxonomy Notes

5. [10 marks] Compare and contrast the three domains of life: Bacteria, Archaea, and
Eukarya. In your essay, discuss the structural, genetic, and ecological differences
and similarities between the three domains, and explain why Archaea were initially
misclassified as bacteria. Use specific named examples to support your points.

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Biology Taxonomy Notes

Answer Key — Multiple Choice (Part A)

1. C 6. C 11. C 16. B

2. C 7. B 12. B 17. C

3. C 8. B 13. C 18. B

4. B 9. C 14. C 19. C

5. D 10. D 15. B 20. B

Answer Key — Cloze (Part B)

1. identification; classification

2. taxonomist

3. Father of Taxonomy; 1735

4. Bacteria; Archaea; Eukaryota

5. genus; species

6. Homo sapiens; genus; species

7. species

8. Genus; species

9. capsid

10. bacteriophage

11. protein ghost

12. interbreeding; reproductively

13. 1942

14. Ernst Haeckel; 1886

15. cell wall; membrane

16. malaria

17. Phaeophyta; Rhodophyta

18. diatoms; silica

19. electron

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Biology Taxonomy Notes

20. thermoacidophiles

End of Taxonomy Study Guide — SMNS Biology Department

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