SBI 3UI Biology - Unit 1 Diversity of Living Things (Chapter 2)

Kingdom Archaea

Organisms in this kingdom are referred to as

“**extremophiles**” because they often love extreme conditions

Habitat of Archaea

Environments with extreme conditions (high temperatures, high acidity, high salinity, etc)

* Can also be found in less extreme environments (eg. human gut)

Archaea

* Unicellular, prokaryotic organisms

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Differences between archaea and bacteria:

* Have genes not found in bacteria
* Genes & proteins that control protein synthesis are very similar to those in Eukaryotes

4 Groups of Archaea (based on their metabolism)

1. Methanogens
2. Halophiles
3. Thermoacidophiles
4. Psychrophiles

Methanogens

(Group of Archaea)

* Produce methane as waste
* Live in anaerobic (oxygen-free) environments
* Use carbon dioxide, nitrogen gas, or hydrogen sulphide as a source of energy

Halophiles

(Group of Archaea)

* Live in extremely salty environments (up to 37% salt concentration)

Thermoacidophiles

(Group of Archaea)

* Live in extremely hot (above 50°C) and acidic environments
* Can live in volcanoes and hot springs

Psychrophiles

(Group of Archaea)

* Cold loving (grow best at -10 to -20 degrees Celsius)
* Found mostly in the Arctic Oceans, Antarctica and cold ocean depths

Kingdom Eubacteria

Facts:

* **Ubiquitous** (found everywhere)
* There are 10 bacteria per every cell that makes up your body
* Play a key role in the cycling of nutrients throughout the biosphere
* Can be harmful, helpful, harmless
* Cyanobacteria are photosynthesizing bacteria that provide a good portion of the world’s oxygen

Bacteria Characteristics

* Prokaryotic
* Have cell walls
* Unicellular (single-celled)
* Heterotrophic or Autotrophic
* ex. *Staphylococcus aureus*

Classifying Bacteria

1. By Shape
2. By Gram Stain
3. By Arrangement
4. By Respiration
5. By Nutrition

By Shape

(Classifying Bacteria)

a. Spherical (Coccus, Cocci)

b. Rod-Shaped (Bacillus, Bacilli)

c. Spiral-Shaped (Spirochetes or Spirillum)

By Gram Stain (Cell Wall Composition)

(Classifying Bacteria)

What is Gram-staining?

Gram-staining is a staining process that stains the cell wall of the bacteria. It is a fast diagnostic tool

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2 Outcomes of a Gram stain:

a. A Gram-**positive** organism has a **purple** colour stain and the peptidoglycan layer is **thick**

b. A Gram-**negative** organism has a **pink** colour stain and the peptidoglycan layer is **thin**

Gram-positive

Organism will be stained __purple__ and its peptidoglycan layer is __thick__

Gram-negative

Organism will be stained __pink__ and its peptidoglycan layer is __thin__

By Arrangement

(Classifying Bacteria)

* As single cells (mono)
* As two cells together (diplo)
* In a chain (strepto)
* In a cluster (staphylo)

By Respiration

(Classifying Bacteria)

Bacteria can be classified according to the types of conditions required for cellular respiration.

* **Aerobic** Bacteria - require oxygen
* **Anaerobic** Bacteria - do not require oxygen
* **Obligate** Anaerobes - die when exposed to O2
* **Facultative** Anaerobes - can grow with or without oxygen

Aerobic Bacteria

Require oxygen

Anaerobic Bacteria

Do not require oxygen

Obligate Anaerobes

Die when exposed to oxygen

Facultative Anaerobes

Can grow with or without oxygen

By Nutrition

(Classifying Bacteria)

Bacteria can be classified by how the organism acquires energy (Autotroph vs Heterotroph) and according to the source of energy the bacteria needs (e.g light or chemicals)

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Nutritional Mode:

**Heterotroph**: takes up organic molecules from environment or by eating other organisms

* Habitat: wide variety of environments

**Photoautotroph**: uses sunlight to make carbon dioxide into carbon compounds like sugar

* Habitat: environments where light is abundant

**Photoheterotroph**: takes up organic molecules from environment and by eating other organisms like basic heterotrophs, and also uses light energy

* Habitat: environments where light is abundant

**Chemoheterotroph**: uses energy released through chemical reactions involving ammonia, hydrogen sulphide, and similar chemicals

* Habitat: dark and/or chemically harsh environments (eg. hot springs, mud, deep oceans, digestive systems of animals)

Heterotroph

Takes up organic molecules from environment or by eating other organisms

* Habitat: wide variety of environments

Photoautotroph

Uses sunlight to make carbon dioxide into carbon compounds like sugar

* Habitat: environments where light is abundant

Photoheterotroph

Takes up organic molecules from environment and by eating other organisms like basic heterotrophs, and also uses light energy

* Habitat: environments where light is abundant

Chemoheterotroph

Uses energy released through chemical reactions involving ammonia, hydrogen sulphide, and similar chemicals

* Habitat: dark and/or chemically harsh environments (eg. hot springs, mud, deep oceans, digestive systems of animals)

Movement of Bacteria

* About __half of all prokaryotes__ do __not__ have structures that allow them to move
* Others have a long whip-like “tail” called a __flagella__ to propel them. Baterial may have several flagella (flagellum, sing.)
* Some spiral-shaped bacteria use a __corkscrew motion__
* Others __secrete mucous__ on which they slide

Reproduction and Growth of Bacteria

Bacteria can reproduce quickly under favourable conditions. There are four main methods by which they can reproduce: binary fission, transformation, conjugation, or transduction

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Mode of Reproduction:

* Binary Fission
* Transformation
* Conjugation
* Transduction

Binary Fission

Is the process by which a single bacteria splits into two genetically identical daughter cells

* No genetic mixing or recombination (Asexual)

Transformation

Some bacteria take up pieces of DNA from the environment and incorporate it into their own DNA

* Yes genetic mixing and recombination

Conjugation

Two bacteria cells will temporarily join and directly exchange genetic material

* Yes genetic mixing and recombination

Transduction

Viruses that infect bacteria (bacteriophages) carry genes from one cells and inject them into another

* Yes genetic mixing and recombination

Endospores

When resources are too limited for bacteria to survive, many transform into a dormant stage called an endospore

* A think internal wall surrounds the DNA and a small amount of cytoplasm
* The cell disintegrates, but is able to survive without water, nutrients, extreme temperatures and most poisons for many years
* *Bacillus anthracis* (causes the disease anthrax) is an example of a bacterium that can do this

Harmful bacteria

* *Salmonella* or *E. coli* causes food poisoning
* *Salmonella typhi* causes typhoid fever
* *Neisseria meningitidis* causes meningitis

Helpful bacteria

* *Streptomyces* produces useful antibiotics as well as other valuable pharmaceutical products
* *Rhizobium* form root nodules on legume plants and enhance plant growth through nitrogen fixation which is beneficial to agriculture
* *Lactobacillus* helps break down food, absorb nutrients, and fight off “bad” organisms that might cause diseases

Major Differences between Viruses and Bacteria

* Viruses cannot live independently outside of cells
* Are extremely small. They are much smaller than cells, even bacterial cells

Characteristics of Viruses

* Not living organisms
* Are functionally dependent on the internal workings of cells
* Viruses invade cells and use them as a host to function and replicate
* Are dormant outside of cells
* Have no cytoplasm, organelles, or cell membrane
* Do not carry out respiration or other life processes
* Do not grow or respond to stimuli
* Consist of a few strands of DNA and/or RNA surrounded by a protective protein capsid

How Viruses are Classified

* By Shape
* Polyhedral
* Spherical
* Cylindrical
* Complex
* By the types of disease they cause
* By the type of organism they infect
* By the type of nucleic acid they have

Bacteriophage

A virus that attacks and infects specific bacterial cells. Only the genetic material enters the host cell

Non-Enveloped Viruses

Do not have a coating made from the cell membrane of a host cell

Enveloped Viruses

Do have a coating made from the cell membrane of a host cell which protects the inner nucleic acid and helps the virus avoid the host’s immune system

The Infectious Cycle

The process by which a virus infects, replicates, and destroys the host cell

* Viruses only become active when their genetic material has enter and taken control of a living cell

The Lytic Cycle

1. Attachment and Entrance

They attach to a host cell and enter it

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2. Protein and Nucleic Acid Replication

The virus uses the cell to make proteins and its own DNA or RNA

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3. Assembly

All the parts of the virus are made and assembled by the infected cell

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4. Release of New Virus Particles

The new virus particles are released from the host cell and the host cell dies (lyses - breaks open) but the virus goes on to infect neighbouring cells

Lysogenetic Cycle

During this cycle, the viral DNA can stay in a dormant state for many years called **lysogeny**. The bacterium continues to grow and divide normally but each time it divides, it makes a __copy of the virus DNA__ that was inserted within its own chromosome.

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When triggered by a __change within the cell’s environment, the viral DNA becomes active__, separates from the bacterial chromosome, and enters the lytic cycle

Vaccines

A substance made from a weakened or dead version of a disease used to trigger the body’s immune system without exposing humans to the full strength disease

Live attenuated vaccines

* Difficult to make
* Because they are live and quite powerful, people with weaker immune systems can’t have them

Inactive vaccines

* Don’t create long-lasting immunity

Active Immunity

Results when a person is exposed to a disease that triggers the immune system to produce antibodies to that disease

* Takes time to develop but is long-lasting

Passive Immunity

Provided when a person is given antibodies to a disease rather than producing them through their own immune system

* Provides immediate protection but only lasts for a short period of time

3 Groups within the Protist Kingdom

1) Animal-like protists (**Protozoa**)

2) Plant-like protists (**Algae**)

3) Fungi-like protists (**Slime Moulds/Water Moulds**)

Characteristics of Protists

* Unicellular
* Eukaryotic
* Aerobic
* Reproduce asexually through mitosis
* Thrive in most environments

Characteristics of Animal-Like Protists (Protozoa)

* Heterotrophs - either engulf their food via **phagocytosis** or absorb nutrients via **diffusion**
* Unicellular
* No cell walls
* Most of motile (able to move)
* Live in moist environments
* Some cause disease

4 Main Groups of Protozoa

1) Sarcodines (sarcodina)

2) Flagellates (zoomastigina)

3) Sporozoans

4) Ciliates

Sarcodines

* Use **pseudopods** (limb-like extensions of cytoplasm) for movement
* Ex. Amoeba

Flagellates

* Move using **flagella**
* Ex. Giardia, Trypanosoma

Sporozoans

* Mostly **parasites**
* Form “**spores**” at some point in their life cycle
* Ex. Plasmodium - causes malaria

Ciliates

* Are “**ciliatea**” (have cilia)
* Usually large
* Ex. Parameciu

Plant-Like Protists (some called Algae)

These protists are “plant-like” because they contain **chlorophyll** and can perform **photosynthesis**. However, if food isn’t available, these protists can eat other organisms (autotrophs and heterotrophs)

6 Main Groups of Plant-Like Protists

1. Dinoflagellates
2. Diatoms
3. Red Algae
4. Brown Algae
5. Green Algae
6. Euglenoids

Dinoflagellates

* Unicellular
* __Photosynthetic__
* Have __two flagella__
* Can reproduce quickly to form a “red tide” which is toxic

Diatoms

* Unicellular
* __Photosynthetic__
* Most abundant in the oceans
* Biggest component of __plankton__ therefore a __major food source__
* Have a ridge cell wall made of __silica__

Red Algae

* Multicellular (also called seaweed)
* Found mainly in warmer seawater
* __Branched with feathery fronds__
* Able to __grow at greater depths__ in the water than other algae since their pigments __absorb the longer wavelengths of light__ which penetrate deeper below the surface

Brown Algae

* Multicellular (also called seaweed)
* Larger than red algae
* __Large, flat fronds__ are able to __withstand pounding of tides__
* __Mucilage-like material__ in cell walls __helps retain water__ when exposed to air at low tide
* Kelp is a member of this group

Green Algae

* Multicellular
* Most plant-like
* Have the same types of chlorophyll as land plants
* Cell walls have cellulose
* Store food reserves as starch
* Found in freshwater and damp places
* Example: Volvox
* Live in freshwater
* Composed of thousands of interdependent flagellated cells
* Other examples include sea lettuce (Ulva), *Spirogyra* and *Chlamydomonas*

Euglenoids

* Unicellular
* Found in freshwater
* Have __two flagella__, one much longer than the other
* About half have __chloroplasts__ (autotroph), the other half are __heterotroph__
* Example: Euglena

Fungi-Like Protists (Slime & Water Moulds)

These protists are difficult to classify because they have characteristics of protozoa, plants and fungi

* Like protozoa, they are “motile” and ingest food
* Like plants, they have cellulose cell walls
* Like fungi, they produce spores

3 Main Groups of Fungi-Like Protists

1) Acellular Slime Moulds (Acrasiomycota)

2) Cellular Slime Moulds (Myxomycota)

3) Water Moulds (Oomycota)

Acellular Slime Moulds

* Exist as individual “**amoeboid**” cells with one nucleus each
* Like protozoa, __ingest bacteria or yeast__
* When food is scarce, can come together and form **pseudoplasmodium** which is a jelly-like mass which produces **spores**

Cellular Slime Moulds

* Visible to naked eye as tiny “slug-like” organisms
* This “blob” is called a **plasmodium** which is multicellular and contains many nuclei

Water Moulds

* Are “**filamentous**” organisms that resemble fungi
* Most live on __dead organic matter__
* Some are **parasites**
* One species, Phytophthora infestans, infect potatoes (responsible for Irish potato famines)