Diversity & ClassificationPart 1

Taxonomy, Bacteria, & Viruses

DIVERSITY & CLASSIFICATION

• Taxonomy is the science of grouping organisms on the basis of their similarities. It was first proposed by Aristotle in 350 BC. He only had 2 groups 1) Plants & 2)Animals.

• In the 1750s Linnaeus developed a new classification system that revolutionized taxonomy. He developed a 2-word Latin name for each species. This is called binomial nomenclature. The genus is the 1st word (1st letter is capitalized) & the species is the 2nd word (1st letter is lower case) – underline the entire thing. Example:Homo sapiens

• The scientific name is universal & is written in Latin. This name is used when dealing with scientists throughout the world because it is universally understood. The common name is what the layperson would call the organism.

• There are 8 levels of classification (taxa):1. Domain

• 2. Kingdom3. Phylum4. Class5. Order

• 6. Family7. Genus8. Species

• (Dumb King Phillip Came Over For Good Sandwiches)

3 Domains

• Domain Bacteria – All eubacteria

• Domain Archaea – All archaebacteria

• Domain Eukarya – All eukaryotes – protists, fungi, plants, & animals

• As one proceeds from kingdom to species, there is an increase in similarities between organisms. Kingdoms hold the greatest numbers of individuals – as you move down, you decrease in number. Each of the foregoing divisions represents a smaller more closely related or similar group of animals than the division just above it.Biologists study chromosome structure, reproductive potential, biochemical similarities, & embryology to determine relationships between organisms. Classification systems are constantly modified as more is learned about organisms.

• A species is a group of individuals agreeing in form, habit, & offspring. Ernst Mayr defined a species as a group of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups. Species typically produce fertile offspring.

Liger = Male lion & female tiger

Tiglon = Male tiger & female lion

Leopon = Female lion & male leopard Zedonk – Female donkey

& Male Zebra

• There are 6 kingdoms:1. Archaebacteria – unicellular prokaryotes – survive in harsh conditions2. Eubacteria –unicellular prokaryotes – “traditional bacteria”

• 3. Protista – eukaryotes – miscellaneous category4. Fungi – eukaryotes – mushrooms, yeast, molds 5. Plantae – eukaryotes - plants6. Animalia –eukaryotes - animals

• Phylogeny is the evolutionary history of a speciesCladistics - relationships are inferred based on similarities derived from a common ancestorCladograms – show the evolutionary relationships among groups of organisms Outgroup - is the distantly related organisms (has the fewest traits in common with the others)Ingroup - the organisms being evaluated (use synapomorphs to evaluate a cladogram)

•A tool to identify organisms is

called a dichotomous key.

•It is made from pairs of

contrasting characteristics (e.g.,

has wings/does not have wings).

22.1

Wacky People Key1a Two feet 21b Some other number of feet 32a Does not look at all human 42b Looks a lot like a human 53a One leg 63b Three or four legs 74a Fly-like Mosk Cara4b Not fly-like 85a Seems to be a girl Rita Nita5b Not a girl 96a Leg is curled , two feet Ru-ela.Brella 6b Leg is straight, one foot Giggles7a Three legs 107b Four legs 118a Has webbed feet Hex Oculate 8b Clawed feet 129a Curly hair, no toes Lugio Wirum9b Wiggly looking mouth, three toes on feet C. Nile10a Very long nose, open mouth Elle E. Funk10b Some other appearance 1311a Has duck bill, two pinchers Tri D. Duckt11b No arms or pinchers 1412a Has ears, tail, and beak Grif Leon12b Four eyes on stalks Eggur Ondy13a One eye, webbed feet Cue Kide13b Four stalked eyes, four pinchers Quadrumenox14a Three toed feet, nose like a flower Tunia petalos14b Spider-like, has spots Patterned mulywumpus

A A cladogramcladogram is a tree-like is a tree-like

diagram diagram showing showing

evolutionary evolutionary relationshipsrelationships

.. Any two branch Any two branch

tips sharing the tips sharing the same immediate same immediate node are most node are most closely related.closely related.

VIRUSES• A virus is a microscopic life form that

reproduces only inside a host. They exhibit some but not all of the characteristics of living things. Viruses contain protein & nucleic acids A host is the living cell in which the virus reproduces. In 1933, Wendell Stanley discovered that viruses are chemicals & not living things with his experiment with Tobacco Mosaic Virus.

• Viruses range in size from 0.01 um to .3 um. They consist of 2 parts:1)inner core of nucleic acids & 2) outer protein coat. The inner core contains DNA or RNA (never both). The capsid is an outer protein coat that makes up 95% of the body of the virus. The envelope is a membrane that surrounds the capsid & helps it to gain entry into cells (it contains proteins, lipids, & glycoproteins derived from the host cell).

• A bacteriophage is a virus that invades bacteria. It attacks by adhering to a cell wall & injecting its nucleic acids that alter the bacterium’s genetic code. Animal viruses enter their host through endocytosis.

• The reproductive cycle of a virus consists of 2 cycles: the lytic cycle & the lysogenic cycle. The lytic cycle consists of the virus killing the host. It has 5 stages.

•1. Adsorption- the phage attaches itself to the cell wall – a chemical bond forms between sites on the tail of the virus & sites on the cell wall – this is like a lock & key

• 2. Entry- The phage releases enzymes that break down the wall – the tail is forced through the weakened wall – the nucleic acid of the phage passes through the hollow tail into the host – the empty capsid is left outside 3. Replication- the virus copies itself in the cell – DNA or RNA enters the host’s chromosomes & makes a template from its own – the organism now makes viral proteins & viral RNA

• 4. Assembly - viral nucleic acids & proteins are assembled into new particles called virions

• 5. Release - new phages release an enzyme that weakens the cell wall – the host cell lyses & releases newly created viruses- up to 300 new viruses can be produced in 1 cell

• The Lysogenic cycle is considered to be an inactive cycle & may stay this way for several generations. It has 3 stages.1. Attachment - the nucleic acids of the invading phage attach to the DNA of the host cell – this is now called a prophage

• 2. Replication - the prophage is now replicated along with the DNA of the host

• 3. Activation - the prophage enters the lytic cycle & makes new viral parts

• Pathogens are disease-causing organisms. Virulence refers to the ability to cause disease. A virus’ virulence depends on 1) Ability to attach to host, 2) speed of reproduction, & 3) response of the host’s cells. The body’s natural defense against disease is referred to as immunity.

• Cells called phagocytes engulf & destroy invading organisms. An antigen is a foreign protein or virus while antibodies are produced by the body to fight them. Active immunity is achieved when the body has actually been exposed to antigens through the pathogen itself or through a vaccine. This process stimulates the production of antibodies. Passive immunity is received from the antibodies produced in another person or animal that has developed immunity. This is only temporary.

• Interferon is a protein that interferes with viral replication. This protein attacks any type of virus but is species specific.

• A retrovirus is deadly because it transcribes DNA from an RNA template & inserts this into the host. This is made possible by reverse transcriptase. These viruses can have a lengthy latent period. Examples are HIV & Herpes.

Prions are “protein infectious particles” that contain no DNA or RNA. These typically infect the brain (mad cow disease).

Symptoms such as depression, difficulty walking, and dementia occur and progress rapidly.

KINGDOMS EUBACTERIA & ARCHAEBACTERIA

• Bacteria are 1- celled organisms that live everywhere. They are the oldest life forms on Earth. E. coli is the most studied bacterium. All bacteria are prokaryotic meaning they have no true nucleus (they do still have genetic material). Bacteria do contain cell walls containing acids & sugars that provide support as well as a cell membrane inside of this cell wall. Some antibiotics work by attacking this structure.

KINGDOM ARCHAEBACTERIA

• Anaerobic & aerobic bacteria adapted to environments with extreme temps, acidity, or salt content; differ from eubacteria in structure of cell wall & cell membrane – RNA polymerase & ribosomal protein very similar to eukaryotes (believed to be more closely related to eukaryotes than eubacteria) – asexual reproduction only

Examples of Archaebacteria

• Thermophiles

• Acidophiles

• Halophiles

Habitat of Archaebacteria

• Extreme environments – swamps, deep seas, cow stomachs, sewage treatment, Dead Sea, volcanoes, geysers

Nutrition Methods of Archaebacteria

• Can be heterotrophic or chemosynthetic. Cyanobacteria are photosynthetic.

KINGDOM EUBACTERIA

• No membrane-bound organelles, nutrition by absorption (some are photosynthetic or chemosynthetic), reproduce by fission or budding.

Bacteria come in 3 primary shapes

• 1. Cocci - sphere-shaped

•2. Bacillus - rod-shaped

• 3. Spirilla - corkscrew-shaped

Bacteria may also be classified based on their shapes in a group

• These include1. Diplo - found in pairs

• 2. Staphylo - found in clusters

•3. Strepto - found in chains

• The walls of bacteria can be either rigid or flexible. Some produce a slime layer known as a capsule. This structure protects the bacterium from the immune system. Bacteria may also be classified as Gram positive or Gram negative based on their colors after a Gram stain.

• Those that are Gram positive stain purple because of a thick peptidoglycan layer in the cell wall (treat these with pencillin). Those that are Gram negative stain pink because the outer membrane is removed by the alcohol rinse & the peptidoglycan layer allows the dye to leave (treat these with tetracycline).

• Bacteria contain many ribosomes & plasmids that are small segments of DNA. Some bacteria may have flagella while others may have pili that resemble cilia. These allow the bacteria to attach to food. Some bacteria are motile while others cannot move. Some bacteria are heterotrophic while others make their own food & are therefore considered to be autotrophic.

• Some bacteria are saprophytic which means they feed on dead organisms. Those bacteria that require oxygen to live are called obligate aerobes. An example is Tuberculosis. Those that can survive without oxygen are termed obligate anaerobes. An example is Botulism. Those that can live with or without oxygen are termed facultative anaerobes. An example is E. coli.

• A colony is a large group of bacteria living together. All members are descendants of a single bacterium.

• Some bacteria form endospores when conditions are harsh. The bacterium makes a membrane around itself when food or nutrients become low. The membrane wraps around one strand of DNA & some cytoplasm & becomes dormant.

Reproduction of bacteria• Asexually – binary fission, budding (some can

also use transformation, transduction, & conjugation)

• Most bacteria can reproduce at a rate of every 20 – 30 minutes. This occurs through the process of fission usually, but may also occur through the process of conjugation. In this process a donor bacterium transfers genetic material to an acceptor bacterium through direct contact .

BACTERIA IN NATURE • Bacteria help the ecosystem recycle

nutrients. Because they break down materials, they are known as decomposers. They play a significant role in sewage treatment. Bacteria also are involved in Nitrogen fixation, a process where they convert atmospheric nitrogen into a form plants can eventually use. Humans also use bacteria to produce yogurt, cheese, pickles, sauerkraut.