Difficulty: Introductory | Prerequisites: Scientific Method, Classification and Evolution notes.
This unit covers how life is organised at the broadest level (the three domains), how organisms obtain energy, the differences between prokaryotic and eukaryotic cells, the nature of viruses, and the diversity of protists. If you have not reviewed classification and evolutionary theory, start there.
All life falls into three domains: Bacteria, Archaea (both prokaryotic), and Eukarya (cells with a nucleus). Organisms fuel themselves in fundamentally different ways, from eating organic molecules to harvesting light or inorganic chemicals. Viruses sit outside this scheme entirely because they cannot reproduce on their own, and protists are the most diverse grab-bag of eukaryotes, ranging from algae to amoebae to slime moulds.
Prokaryote
A unicellular organism lacking a membrane-bound nucleus and membrane-enclosed organelles. Think of it as the simpler, older cell design: DNA floats in the cytoplasm rather than being sealed inside a nucleus.
Eukaryote
An organism whose cells contain a membrane-bound nucleus and organelles such as mitochondria and (in plants) chloroplasts. In simple terms, these are the more complex cells that make up animals, plants, fungi, and protists.
Bacteria (domain)
Ubiquitous prokaryotes with diverse metabolisms and cell walls containing peptidoglycan. They are found in virtually every habitat on Earth.
Archaea (domain)
Prokaryotes that resemble bacteria in size and shape but have distinct cell wall compositions (no peptidoglycan) and unique biochemistry. Often found in extreme environments such as hot springs, salt lakes, and deep-sea vents.
Eukarya (domain)
The domain encompassing all organisms with eukaryotic cells: plants, animals, fungi, and protists.
Peptidoglycan
A polymer of sugars and amino acids that forms the rigid mesh in bacterial cell walls. Think of it as the scaffolding that gives bacteria their shape.
Binary fission
The asexual reproduction method of prokaryotes, in which a single cell divides into two genetically identical daughter cells.
Endospore
A tough, dormant structure formed by some bacteria to survive harsh conditions such as extreme heat, desiccation, or chemical exposure.
Virus
A particle of genetic material (DNA or RNA) enclosed in a protein coat (capsid) that cannot reproduce independently and must hijack a host cell's machinery. Not classified within the three domains because it lacks cellular structure and metabolism.
Capsid
The protein shell surrounding a virus's genetic material.
Glycoprotein
A protein with attached sugar chains found on the surface of viruses (and some cells), used to recognise and bind to host cells during infection.
Mitochondria
Membrane-bound organelles in eukaryotic cells responsible for producing energy via cellular respiration. Often called the "powerhouse of the cell."
Chloroplast
An organelle found in plant cells and some protists that carries out photosynthesis, converting light energy into chemical energy.
Endosymbiotic theory
The hypothesis that mitochondria and chloroplasts originated as free-living prokaryotes that were engulfed by ancestral eukaryotic cells and eventually became permanent organelles. Supported by the fact that both have their own DNA and double membranes.
Chemoheterotroph
An organism that obtains both energy and carbon from organic molecules. Most animals and fungi are chemoheterotrophs.
Chemoautotroph
An organism that derives energy from inorganic chemical reactions and fixes inorganic carbon. Some archaea and deep-sea bacteria use this strategy.
Photoheterotroph
An organism that uses light for energy but relies on organic compounds for carbon.
Photoautotroph
An organism that uses light for energy and fixes inorganic carbon (CO2). Plants and algae are the classic examples.
Protist
A diverse, mostly unicellular eukaryote that does not fit neatly into the plant, animal, or fungus kingdoms. Think of it as the "everything else" category of eukaryotic life.
Bacteria – prokaryotic, cell walls with peptidoglycan, diverse metabolisms, found everywhere
Archaea – prokaryotic, distinct cell wall composition (no peptidoglycan), often inhabit extreme environments (thermophiles, halophiles, methanogens)
Eukarya – eukaryotic cells with membrane-bound nuclei; includes plants, animals, fungi, and protists
Organisms are classified by their energy source and carbon source:
Chemoheterotrophs – energy and carbon from organic molecules (most animals, fungi)
Chemoautotrophs – energy from inorganic chemicals, carbon from CO2 (some archaea, deep-sea vent bacteria)
Photoheterotrophs – energy from light, carbon from organic molecules (certain purple non-sulphur bacteria)
Photoautotrophs – energy from light, carbon from CO2 (plants, algae, cyanobacteria)
Unicellular, no nucleus or membrane-enclosed organelles
Circular DNA (not linear chromosomes)
Reproduce by binary fission (asexual)
Come in diverse shapes: cocci (spherical), bacilli (rod-shaped), spirilla (spiral)
Can form colonies and produce endospores for survival in harsh conditions
Bacteria play critical ecological roles: oxygen production (cyanobacteria), decomposition, nitrogen fixation
Archaea are structurally similar to bacteria but biochemically distinct, and they thrive in extreme habitats
Consist of genetic material (DNA or RNA) enclosed in a protein coat (capsid)
Lack cellular structure, cannot metabolise, and cannot reproduce independently
Require a host cell: they use surface glycoproteins to bind to the host, then hijack the host's cellular machinery to replicate
Their status as "living" is debated because they do not meet all the standard criteria for life (no metabolism, no independent reproduction)
Not classified within any of the three domains
Eukaryotic cells possess a membrane-bound nucleus and organelles including mitochondria and (in plants/some protists) chloroplasts
Mitochondria produce energy via cellular respiration
Chloroplasts carry out photosynthesis
The endosymbiotic theory proposes that mitochondria and chloroplasts were once free-living prokaryotes engulfed by ancestral eukaryotic cells
Evidence: both organelles have their own DNA, replicate independently, and possess double membranes consistent with engulfment
Protists are a highly diverse, mostly eukaryotic group, often called a "catch-all" kingdom. They are grouped by their resemblance to other kingdoms:
Algae-like protists – photosynthetic, contain chlorophyll A, can be unicellular or multicellular
Protozoan protists – animal-like, heterotrophic, unicellular, lack cell walls
Mould-like protists – fungus-like, often macroscopic, produce spores, heterotrophic by ingestion or absorption
Ecological importance:
Form the base of aquatic food chains
Contribute to global oxygen production
Some produce commercially valuable substances (e.g. antibiotics)
Others are pathogenic (e.g. malaria-causing Plasmodium)
Students often assume Archaea and Bacteria are the same thing because both are prokaryotic. They are distinct domains with different cell wall compositions, membrane lipids, and genetic machinery.
Viruses are frequently called "the smallest living organisms." They are not classified as living because they lack cells, metabolism, and the ability to reproduce on their own.
Students sometimes think "protist" is a single, coherent kingdom. It is better understood as a convenience grouping for eukaryotes that do not fit into the plant, animal, or fungus kingdoms. Its members are not necessarily closely related to one another.
The endosymbiotic theory is sometimes confused with a general idea that cells "cooperate." The specific claim is that mitochondria and chloroplasts were once independent prokaryotes that were physically engulfed and retained.
⚠️ Be able to compare and contrast Bacteria, Archaea, and Eukarya across multiple traits (nucleus, cell wall, membrane lipids, habitats).
⚠️ Know the four energy acquisition modes and be able to classify an organism when given a description of its energy and carbon sources.
⚠️ Understand the evidence supporting endosymbiotic theory (own DNA, double membranes, independent replication).
⚠️ Be prepared to argue both sides of the "are viruses alive?" debate using the criteria for life.
⚠️ Know the three protist sub-groups (algae-like, protozoan, mould-like) and what distinguishes each.
True or False: Archaea have peptidoglycan in their cell walls, just like Bacteria. Answer: False. Archaea lack peptidoglycan.
Fill in the blank: An organism that uses light for energy and CO2 for carbon is called a ______. Answer: photoautotroph.
True or False: Viruses can reproduce independently without a host cell. Answer: False. Viruses require a host cell's machinery to replicate.
Fill in the blank: The endosymbiotic theory proposes that ______ and ______ were once free-living prokaryotes. Answer: mitochondria; chloroplasts.
True or False: All protists are unicellular. Answer: False. Some algae-like protists are multicellular.
Q: Compare the three domains of life in terms of cell type, nuclear membrane, and cell wall composition.
A: Bacteria are prokaryotic (no nuclear membrane) with peptidoglycan cell walls. Archaea are prokaryotic (no nuclear membrane) with cell walls that lack peptidoglycan and contain unique lipids. Eukarya are eukaryotic (membrane-bound nucleus) with varied cell wall compositions: cellulose in plants, chitin in fungi, none in animals.
Q: A deep-sea organism lives near a hydrothermal vent, derives energy from hydrogen sulphide, and fixes CO2. What is its energy acquisition mode?
A: It is a chemoautotroph. It obtains energy from an inorganic chemical (hydrogen sulphide) and uses CO2 as its carbon source.
Q: List three pieces of evidence supporting the endosymbiotic theory.
A: (1) Mitochondria and chloroplasts have their own circular DNA, similar to prokaryotic DNA. (2) Both organelles are surrounded by a double membrane, consistent with engulfment. (3) Both replicate independently of the cell via a process resembling binary fission.
Q: Why are viruses not classified within any of the three domains of life?
A: Viruses lack cellular structure, cannot carry out metabolism on their own, and cannot reproduce without hijacking a host cell. Because they do not meet the standard criteria for life (cells, metabolism, independent reproduction), they fall outside the domain system.
The three-domain framework sets the stage for every biodiversity unit that follows: fungi, plants, and animals are all branches within Eukarya. Endosymbiotic theory connects to genetics and cell division because mitochondria and chloroplasts carry their own DNA and replicate semi-independently. Energy acquisition modes reappear when studying plant photosynthesis (photoautotrophy) and animal nutrition (chemoheterotrophy).
Domains of life, Bacteria, Archaea, Eukarya, prokaryote, eukaryote, peptidoglycan, binary fission, endospore, virus, capsid, glycoprotein, lytic cycle, lysogenic cycle, mitochondria, chloroplast, endosymbiotic theory, endosymbiosis, chemoheterotroph, chemoautotroph, photoheterotroph, photoautotroph, protist, algae, protozoan, slime mould, BIO 101, biological diversity