Taxonomy (Archaea, Bacteria, Protists & Fungi)

The 8 organism classification systems

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

(Dear King Phillip Came Over For Good Spaghetti)

The two parts of binomial nomenclature naming

The organism’s genus (capitalized) followed by the species (lowercase)

• Either italicized or underlined (ex. Homo sapiens OR Homo Sapiens)

Who invented binomial nomenclature

Carl Linnaeus

What’s the point of scientific naming

Scientific names are more specific than general names and provide a common language for researchers everywhere

What’s a dichotomous key

A reference tool used to determine the species of an unknown organism.

• The key has a series of choices that leads to the identification of the species

The Six Kingdoms are:

Archaea, Bacteria, Protista, Fungi, Plantae, Animalia

Taxonomy is

The branch of biology that deals with the classification of living organisms

Originally there were only __ categories for all living organisms

2. Plants and Animals (Aristotle divided them into plants being stationary and photosynthetic, and animals being motile and food-ingesting)

Domains are based on

RNA (a form of genetic information)

The three domains are

Bacteria, Archaea, Eukarya

6 Differences between Prokaryotes and Eukaryotes

(Inclusion, Size, Organelles, Cell Division, Reproduction, Cell Number)

1. Prokaryotes include domains bacteria and Archaea and Eukaryotes are the other 4 kingdoms

2. Prokaryotes are very small and eukaryotes are larger in comparison (10x)

3. Prokaryotic DNA are circular are not membrane-bound while Eukaryotic are linear and membrane-bound, forming a nucleus

4. Prokaryotes divide not by mitosis or meiosis and eukaryotes divide by mitosis and meiosis

5. Prokaryotes commonly reproduce Asexually while Eukaryotes commonly reproduce sexually

6. Prokaryotes are usually unicellular and Eukaryotes are mostly multicellular

4 Traits of Kingdom Bacteria and an Example

(Cell Type, Cell Number, Nutrition, Cell Walls)

• Prokaryotic Cells (no nucleus)

• Unicellular (though sometimes live in colonies)

• Autotrophs or Heterotrophs

• Cell walls contain peptidoglycan

  • Ex. Streptococcus, E. coli

4 Traits of Kingdom Archaea and an Example

(Cell Type, Cell Number, Nutrition, Cell Walls)

• Prokaryotic Cells

• Unicellular

• Autotroph or Heterotroph

• Cell walls do NOT contain Peptidoglycan

  • Ex. Extremophiles, Halophiles, Acidophiles, Methanogens

5 Traits of Kingdom Protista and an Example

(Cell Type, Cell Numbers, Nutrition, Cell Walls, Special)

• Eukaryotic Cells

• Most are Unicellular

• Autotrophs or Heterotrophs

• Cell walls contain cellulose; some species contain chloroplasts

• The most diverse kingdom, recently organized into supergroups to further differentiate

  • Ex. Amoeba, Paramecia, Slime moulds

4 Traits of Kingdom Fungi and an Example

(Cell Type, Cell Walls, Nutrition, Cell Walls)

• Eukaryotic Cells

• Mostly multicellular

• Heterotrophs

• Cell Walls contain Chitin (a polysaccharide)

  • Ex. Mushrooms, yeast, mould

Cell Structure Differences between Archaea and Bacteria

• Bacteria have cells walls made up of the polymer Peptidoglycan while Archaea do not

• The plasma membrane of archaea are made up of lipids which are distinct from bacteria’s

• The ribosomal proteins of archaea are similar to those in eukaryotic cells not those in bacteria

The 3 main prokaryotic shapes

Cocci - Round (singular is coccus)

Bacilli - Rod-shaped (Singular is Bacillus)

Spirili - Spiral-shaped

Some forms don’t fit into these types like cubes, pyramids, rods with stars, rectangles, etc.

The 3 prokaryotic prefixes

Diplo - Arrange themselves in Pairs

Staphylo - Arrange themselves in Clusters

Strepto - Arrange themselves in Chains

2 Ways which prokaryotes obtain energy

Methanogensis

• Unique to Archaea

• Produces methane as a byproduct

• Methane-producing archaea live in the digestive tract of cattle, landfills, and swamps

• Anaerobic

Photosynthesis

• Unique to Bacteria

• Cyanobacteria use solar energy to convert carbon dioxide and water into sugar and oxygen

• These bacteria are abundant in both fresh and saltwater

Habitual Differences and Similarities of Bacteria and Archaea

• Both can occupy environments with oxygen (aerobic) and without (anaerobic)

• Most Bacteria are Mesophiles - Occupy environments with moderate conditions

• Some Archaea are Extremophiles - Occupy environments with extreme conditions

  • Thermophiles - Live in hot springs and deep-sea vents (over 100 degrees Celsius)

  • Acidophiles - live in volcanic craters and mine drainage lakes (as low as pH under 3)

  • Halophiles - live in salt lakes and inland seas (salt concentrations above 20%)

Reproduction of Archaea and Bacteria

• Both domains are prokaryotic and lack nuclei; both reproduce asexually by binary fission

  • As a cell grows, it makes a copy of a single chromosome. After elongating and separating the two copies, the cell builds a septum between them and splits into 2 identical cells

• DNA can be exchanged during Conjugation

  • One cell links to another by a pilus (tube) and transfers a copy of some or all of the chromosomes

Bacteria & Human Health

Some can harm it. Ex. Streptococcus Pyogenes (strep throat), Streptococcus Mutans (tooth decay)

Some can help: Aid digestion, support the immune system, protect against pathogens.

Bacteria & The Environment

Many are Decomposers

• They break down organic molecules and release carbon, hydrogen, nitrogen, sulfur

  • Therefore, supporting those nutrient cycles

    • Ex. Cyanobacteria - Major producers of oxygen on Earth

Archaea and Biotechnology

• Archaea contain enzymes that allow them to function perfectly in extreme conditions

• PCR is a tech that can produce millions of copies of a DNA sequence

  • By switching to heat-resistant DNA polymerase from archaea, the PCR process became fully automated, cheaper, and faster.

    • This transformed modern biotech and medical diagnostics.

The Evolution of Eukaryotes

The theory of Endosymbiosis suggests that eukaryotic cells evolved from symbiotic relationships between two or more prokaryotic cells.

• Chloroplasts and Mitochondria may have been free-living prokaryotes that simply continued their functions inside the cell

Evidences

• Those organelle membranes, ribosomes, circular chromosomes and gene sequences closely match those of living prokaryotes

• Both organelles reproduce by binary fission

• Both contain their own internal genetic material separate from the cell’s DNA, indicating ancestral independence

What are protists?

Any eukaryotic organism (with a nucleus and complex cell structures) that is not an animal, plant, or fungus

Evolution order from prokaryotes

Prokaryotes (endosymbiosis) → Single celled Eukaryotes → 1st multicellular organism → Complex Eukaryotes

How did multicellular organisms evolve?

Evolved from colonies created by dividing individual cells

• Different functions developed among different groupings of cells (ex. absorbing nutrients, gathering information from the environment)

The 3 types of Protists

1. Animal-like (Protozoans)

2. Fungus-like

3. Plant-like

What are Animal-Like Protists?

Protozoans: animal-like because they consume other organisms for food

2 types of Animal-Like Protists

The Cercozoans & The Ciliates

What are Cercozoans?

• Most familiarly Amoeba

  • Change their shape using the internal cytoskeleton to move and create different forms (pseudopods, “false feet”)

  • Amoebas live in salt and freshwater, mud, some are parasites living in animal hosts

What are Ciliates?

• Have short hair-like projections called cilia that cover the cell’s surface

• Used for locomotion and collecting food particles on the surface to move them into the cell

  • Some are free-living (ex. Paramecia)

  • Some are parasites (ex. Balantidium Coli - lives in large intestine, causes diarrhea)

What are Fungus-Like Protists?

• Heterotrophs

• Produce Spores

• Have a unique cell wall different from kingdom fungi

2 types of Fungus-Like Protists

Plasmodial Slime Moulds & Water Moulds

What are Plasmodial Slime Moulds?

• Visible to the unaided eye as tiny slug-like organisms

• Creep over damp, decaying plant material in forests and fields

• Contains many nuclei

• Feed by engulfing small particles of food into their cytoplasm (like Amoeba)

What are Water Moulds?

• Most live on dead organic matter

• Some are parasites on fish, insects and plants

• Extend fungus-like threads into their host’s tissues, where they release digestive enzymes and absorb the resulting nutrients

What are plant-like protists?

Protists that make their own food by photosynthesis

2 types of Plant-Like Protists

Diatoms & Dinoflagellates

What are Diatoms?

• A type of Phytoplankton (single-celled, free-floating aquatic organisms)

• Rigid Cell Walls that fit together like a box with a lid

  • (with an outer layer of silica, a common ingredient in sand and glass)

• Usually reproduce asexually by mitosis

  • They are an important food source for larger marine organisms

What are Dinoflagellates?

• A type of Phytoplankton

• Have two flagella at right angles to each other (used to spin through water)

• Can reproduce very quickly with plentiful nutrients (Known as Algal Blooms)

• Some species live inside other organisms, like Coral

  • The protists gain nitrogen waste and carbon dioxide from the coral, and the coral gains the benefits of the photosynthetic protists

• If ocean temperatures rise, this relationship breaks down, killing the coral (coral bleaching)

What is the Kingdom Fungi

Eukaryotic organisms that are distinct from plants and animals (Ex. yeast, mold, mushrooms)

There are more than ________ species in the kingdom ranging from _____ to ______.

100,000, Unicellular, Multicellular

How do fungi feed?

Release enzymes into their surroundings, then absorb nutrients into their cells (Extracellular Digestion)

The 4 ways fungi obtain nutrients

Parasitic Fungi: Absorb nutrients from the living cells of a host organism. Usually lives in a host

Predatory Fungi: Soil fungi whose mycelia have specialized structures for trapping prey

Mutualistic Fungi: Have partnerships with other organisms. Mycelia usually cover the roots of a plant.

Saprobial Fungi: Decomposers whose mycelia absor nutrients from dead or decaying matter

3 Fungal Reproduction Methods

Varies; Some are sexual, and some are asexual.

• Asexual Budding: Produces one cell from two

• Asexual Fragmentation: Produces a new organism from a separated fragment of mycelium

• Sexual Reproduction: Spore production and release

3 Fungi Phylum

1. Zygospore Fungi

2. Fungi Imperfecti

3. Club Fungi

What are Zygospore Fungi?

• Include food moulds

• Multicellular

• Mostly terrestrial

• Usually asexual reproduction

How do Rhizopus bread molds reproduce under only some circumstances?

• Two haploids of hyphae of opposite types combine and fuse their nuclei

• A thick wall develops (zygospore)

• The zygospore protects contents from drying

• It remains dormant until conditions are favourable for growth

What are Fungi Imperfecti?

• All fungi that do not reproduce sexually at all

• An important source for pharmaceuticals

• The mold Penicillium produces the antibiotic penicillin

• The drug Cyclosporine is derived from an imperfect fungi and is given to patients after transplant surgery to help suppress their immune systems so they don’t reject the transplant organ

• The imperfect Fungal spores growing in some cheese give it a strong flavour

What are club fungi?

• Includes mushrooms and puffballs

• The fruiting bodies of club fungi release spores called basidiospores from club-shaped hyphae called basidia

• The largest part of a club fungus is a vast network of hyphae that spreads underground (mycelium)

  • You can see evidence of hidden mycelium in the circles of mushrooms that sometimes appear on lawns and forest floors

Club Fungus Reproductive Cycle

1. Basidia line the cap’s gills’ surface and release basidiospores

2. When it lands in a suitable environment it germinates and produces a hyphae

3. Hyphae grow into a haploid mycelium into the soil

4. Mycelia from two different mating types come together and the hyphae fuse

5. New mycelium forms with each cell containing a haploid nucleus from each mating type

6. Buttons or compact masses of hyphae form under the soil

7. A button turns into a mushroom

8. Inside each basidium, the haploid nuclei join to form a diploid cell

9. Meiosis occurs, producing four haploid nuclei, each one becoming a basidiospore

10. Basidiospores detach after maturing and are dispersed to new locations

What are lichens?

• Composite organisms.

  • They form a unique organism that depends on a relationship between different species

  • Ex. fungus and a photosynthetic organism like cyanobacterium

• Lichens are an important food for many animals (ex. deer, elk, caribou)

• They are used as a source of natural dye to colour wool and make litmus paper