Classification of organisms

Kingdoms: Eubacteria, Archaebacteria, Protist

and Fungi

classification

• Grouping objects or organisms based on a set of conditions.

• For biologists, doing this with all of the organisms there are on the earth, it makes it easier to study them!

• There are many different ways to group organisms.

Early systems of classification• Aristotle: plant or animal

• Then animals were further classified based on habitat and physical characteristics.

• Plants were further classified by size and structure, trees, shrubs

• This system did NOT take into account the changes and evolutionary history of the organisms.

New systems of classification

• In the 18th century • Carolus Linnaeus developed • Taxonomy• A branch of biology concerned with

naming, identifying and classifying species based on morphological and behavioral similarities and differences.

• Linnaeus gave each organism 2 names • A genus and a species name and called

this binomial nomenclature.

•   A systematic method of classifying plants and animals.

• Classification of organisms based on degrees of similarity representing evolutionary (phylogenetic) relatedness.

Scientific Names

• Binomial nomenclature (Linnaeus)• A 2 name system so that not two organisms will

ever have the same name.

• The genus name is combined with a second name to make the species name unique.

• For example: humans• Genus Homo • Species Homo sapiens

Why 2 names?• The name are Latin ( the language of science)• The first is the genus• The second is the epithet or specific identifying

name. They are both needed to identify the organism.

• Common names can vary but scientific are universal.

• First names are capitalized, second are not.• In books, names are italicized, if hand written

they are underlined. • The genus can be abbreviated with the first letter

Human classification

• Kingdom Animalia

• Phylum (Division for plants) Chordata

• Class Mammalia

• Order Primates

• Family Hominidae

• Genus Homo

• Species Homo sapiens

Levels of classification

• King Philip came over from Germany swimming

KINGDOM

PHYLUM

CLASS

ORDER

FAMILY

GENUS

SPECIES

LARGEST SMALLEST

Domains

• The largest groups

• Eukarya

• Archaea/ Archaebacteria

• Bacteria/Eubacteria

• Each level has more and more similarities!DomainKingdom

Phylum (Division for plants)

Class Order Family Genus

Species

6 Kingdoms

heterotrophautotroph heterotroph

autotroph heterotroph

heterotrophautotroph

How has classification changed?

• Today classification looks at the evolutionary relationships and DNA similarities.

• Many organisms have been reclassified from where they were originally classified as new information is learned.

genus

• A groups of organisms that are closely related and share a common ancestor.

family

• A group of genera that have similar characteristics

species

• Organisms so closely related that they can mate and produce fertile offspring in a natural setting.

• The “biological species concept”• There are exceptions to this definition but it

works for most organisms.• Phylogenetic species: goes with biologic and

says the organisms have evolved independently from an ancestral population.

phylogeny

• The evolutionary history of a species.

• Where did it come from?

• When organisms become isolated they become different, this can lead to new species…

characters• Inherited features that vary among species

• Used by scientists to help put together the evolutionary history of a species: its phylogeny.

• The more shared characters/the more closely related.

• Homologous structures show relationships

• Analogous structures don’t

Understanding phylogenetic trees

• http://www.youtube.com/watch?v=xwuhmMIIspo&feature=youtube_gdata_player

Dinosaurs and birds

• Oviraptor and sparrow

• Feathers, hollow spaces in bones similar bone structures to birds show more similarities to dinosaurs with birds then to reptiles.

DNA sequences

• The more similar the sequences, the closer the relationship between the organisms.

Molecular clocks

• Mutations occur randomly and can be used to determine how long the DNA has been mutating or changing from its original form.

• A major problem with this includes the fact that the genes don’t mutate at a constant rate!

• These are used to try to determine when a divergence from a common ancestor occurred.

cladistics

• A way to study evolutionary relationships.

• It rebuilds phylogenies and hypothesizes evolutionary relationships using shared characters.

• Cladograms show branching diagrams where each species may have originated.

• Kind of like a pedigree!

• http://biology.unm.edu/ccouncil/Biology_203/Summaries/Phylogeny.htm

• Clades show hypothesized phylogeny based on DNA sequences, morphology all of the current information.

• Branches are called nodes.

• The closer to the end like species b and c, the more closely related..

Construction a cladogram video

•  

• http://www.youtube.com/watch?v=46L_2RI1k3k&feature=youtube_gdata_player

Cladograms

Domains

• For now there are 3!

Kingdoms/DomainsArchaea

(Archaebacteria) and

Bacteria (Eubacteria)

Archaea /Archaebacteria

• Prokaryotic• Unicellular• No nucleus

• No peptidoglycan on the cell walls• Some similarities to eukaryotes in the

cytoplasm• Some Autotroph/ most heterotroph

Archaebacteria

• The most primitive group, the archaebacteria, are today restricted to marginal habitats such as hot springs or areas of low oxygen concentration.

Three types of Archaebacteria: methanogens, halophiles, and thermacidophiles. They live in extreme habitats like very salty water!

prokaryotes

Domain and KingdomBacteria/Eubacteria

prokaryotesunicellularno nucleus

cell walls contain peptidoglycansome autotrophs/most heterotrophs

• Organisms in this group lack membrane-bound organelles associated with higher forms of life. Such organisms are known as prokaryotes.

• Their small size, ability to rapidly reproduce (E. coli can reproduce by binary fission every 15 minutes), and diverse habitats/modes of existence make bacteria the most abundant and diversified kingdom on Earth.

• Bacteria occur in almost every environment on Earth, from the bottom of the ocean floor, deep inside solid rock, to the cooling jackets of nuclear reactors.

Rod-Shaped ( Bacillus) Bacterium, hemorrhagic E. coli, strain 0157:H7

Scanning electron micrographs illustrating external features of the

rod-shaped bacterium E. coli.

Coccus round-shaped Bacterium (causes skin infections), Enterococcus faecium

Spiral shape bacteria (spirochete)

Left, a cross-section of a cell illustrating the location of a flagella inside the cell;

Center, Borrelia burgdorferi, the organism that causes Lyme disease; and Right,

Treponema pallidum, the spirochete that causes the venereal disease syphilis.

The image above is from http://www.bact.wisc.edu/Bact303/MajorGroupsOfProkaryotes.

binary fission

Endospores• are a method of survival, not one of

reproduction. Certain bacteria will form a spore within their cell membrane (an endospore) that allows them to wait out deteriorating environmental conditions.

• Certain disease causing bacteria (such as the one that causes the disease Anthrax) can be virulent (capable of causing an infection) 1300 years after forming their endospores

All other Kingdoms are made up of Eukaryotic cells

Domain EUKARYAHAVE ORGANELLES

A NUCLEUS

Evolution of Eukaryotes

• The endosymbiosis hypothesis…

PROTISTS ??eukaryotic

unicellular/ some multiheterotrophic and autotrophic

• New classification??

• Some plant like some animal like.

• This is a great example of how the system is constantly changing based on new information!!!

Classification of Protists

• The protists include heterotrophs, autotrophs, and some organisms that can vary their nutritional mode depending on environmental conditions.

• Protists occur in freshwater, saltwater, soil, and as symbionts within other organisms.

• Due to this tremendous diversity, classification of the Protista is difficult.

Protozoa: Single-Celled, Motile Organisms “animal-like”

• This group of protists are single-celled, motile, heterotrophs.

• Most digest their food by vacuoles formed by phagocytosing other organisms (bacteria or other single-celled creatures).

• Reproduction varies greatly, from a binary fission-like process to true meiosis.

• The main distinguishing feature is the method of locomotion: flagella, cilia, or pseudopodia.

Amoeboid Protozoa Use Pseudopods for Movement

• Amoeba and Pelomyxa move by extensions of their cytoplasm known as pseudopodia.

Foraminifera

• live in the oceans and secrete a shell (also known as a test) composed of silica or calcium carbonate.

• Thus, the fossil record of forams is quite good. Oxygen isotope data from forams has been used to calculate ocean temperature fluctuations over the past 100,000 years.

Sporozoans

• Members of this group cause malaria and toxoplasmosis.

• Toxoplasmosis is transmitted from cats to humans, with between 7 and 72% of the population infected, depending on the geographic area.

Malaria

• infects an estimated 300 million people, and is spread by mosquitoes, transfusions, and shared hypodermic needles.

• Infected individuals can be treated with a variety of medicines. However, some of the sporazoans that cause malaria have developed immunity to some of the more commonly employed medicines.

Ciliates

• Ciliates are complex, heterotrophic protozoans that lack cell walls and use multiple small cilia for locomotion.

• To increase strength of the cell boundary, ciliates have a pellicle, a sort of tougher membrane that still allows them to change shape.

• Most of the 8000 species are freshwater. Most ciliates have two nuclei: a macronucleus that contains hundreds of copies of the genome and controls metabolisms, and a single small micronucleus that contains a single copy of the genome and functions in sexual reproduction.

Paramecium is a common ciliate

ParameciumShowing cillia

“Plant like” ProtistsALGAE

• Photosynthetic Autotrophs

• Single and multicellular

• Phytoplankton are single cell: basis of food chain

• diatoms, dinoflagellates,

Rhodophyta, the Red Algae

• . Carrageenan is an additive to puddings and ice creams; dried sheets of red algae are used in some Japanese dishes.

Phaeophyta, the Brown Algae

Chlorophyta, the Green Algae

diatoms

Red tides

• are caused by population explosions of certain dinoflagellates that release a neurotoxin into the environment.

• Shellfish concentrate this toxin and it can kill people who eat the contaminated shellfish.

Fungus-like Protists

• Slime molds and mildews

Slime Molds

Slime molds are often classified as fungi

Euglenoidsboth “plant and animal –like”

• Usually grouped with the plant like because they have the chloroplasts.

Euglena

FUNGIeukaryotic

unicellular and multicellularheterotrophic

chitin in cell wallscan’t move!

Live in many environments

Fungi • Fungi are almost entirely multicellular (with

yeast, Saccharomyces cerviseae, being a prominent unicellular fungus), Bread yeast

• heterotrophic (deriving their energy from another organism, whether alive or dead), and usually having some cells with two nuclei (multinucleate, as opposed to the more common one, or uninucleate) per cell.

• Ecologically this kingdom is important (along with certain bacteria) as decomposers and recyclers of nutrients.

• Economically, the Fungi provide us with food (mushrooms; Bleu cheese/Roquefort cheese; baking and brewing), antibiotics (the first of the wonder drugs, penicillin, was isolated from the fungus Penicillium), and crop parasites (doing several million dollars per year of damage).

Structures in the bodies of fungi

• Hyphae: filaments

• Fruiting bodies: reproductive structures

• Cell walls made up of chitin

• Mycelium: net like mass of hyphae

• Beer and wine are produced through the action of fungi known as yeasts, such as Saccharomyces cerviseae.

• Many antibiotics are produced by fungi.

• Fungi are important both as a source of food and in the preparation of food. Edible fungi include mushrooms, truffles, and morels. Cheeses such as Gorgonzola, Roquefort, Stilton, and bleu have fungal colonies that give theses cheeses their distinctive flavors.

Reproduction of Fungi

• Budding

• Fragmentation

• spores

Classification of Fungi • Over 60,000 species of fungi are known.

Fungi are classified by their method of reproduction (both sexual and asexual).

• Historically they have been divided into four taxonomic divisions: Chytridiomycota (chytirids), Zygomycota (mold), Ascomycota (Yeast or sac fungi), Basidiomycota (club mushrooms), and Deuteromycota (imperfect).

Mutualistic symbiotic fungal relationships

• Lichens: fungus and algae

• Mycorrhizae: fungus and plant roots

• Genus: Candida Disease(s): Candidiasis

Image Legend: Skin scraping from superficial candidiasis showing clusters of budding yeast cells and branching pseudohyphae.

• Club fungi are important as commercial crops. They also cause many diseases that result in loss or reduction of grain yields.

• Agaricus campestris is the common mushroom found in grocery stores;

• Lentinus edodes is the less commonly bought shitake mushroom: more than $14 billion per year of these products are sold.

• Amanita phalloides is the most poisonous of all mushrooms. Other mushrooms have hallucinogenic properties (such as the drug psilocybin) important in native religious rituals in Central and South America.

Athlete's foot

• Genus: Epidermophyton Species: floccosumDisease(s): Athlete's footTitle: Tinea pedisImage Legend: The disease is unusual because the nails are also involved.

Genus: Trichophyton Species: verrucosum

Disease(s): Dermatophytosis, Tinea barbae

Title: Dermatophytosis of the beard areaImage Legend: Severe tinea barbae caused when the patient rubbed

against cattle.

Genus: Microsporum Species: gypseum

Disease(s): RingwormImage Type: Microscopic Morphology

Title: Macro- and microconidiaImage Legend: Macro- and microconidia. Lactophenol cotton blue, phase contrast

microscopy, 630X.

Genus: Microsporum

Species: canisDisease: Tinea

Title: Ringworm lesionsImage Legend:

Ringworm lesions developed after an exposure to a cat

having ringworm.

Genus: Saccharomyces Species: cerevisiae

Disease (s): Disseminated infection VulvovaginitisImage Type: Microscopic Morphology

Title: Acid fast stainImage Legend: Asci, containing broadly elliptical

ascospores

Color enhanced.

Bread mold

plantae

• Multicellular

• Eukaryotic

• Cell walls with cellulose

• Autotrophic photosynthetic

• Some are heterotrophs

• Live in water and on the land

• Can’t move

Animals/Animalia

• Multicellular

• Eukaryotic

• Without cell walls

• Heterotrophs

• Live in water and on land

• Most can move / at least at some point in their life

Viruses

adenovirus

The Adenovirus is a DNA virus that causes colds and "pink eye".

                                                                                                               

The Papillomavirus is a DNA virus that causes warts.

The Influenza virus causes the flu. It has RNA as its

genetic material instead of DNA.

• Bacteriophages invade the host cell, take over the cell, and begin replicating viruses, eventually lysing or bursting the host cell, releasing the new viruses to infect additional cells.

•

Lysogenic cycle

Lytic Cycle

Retroviruses

• Retroviruses have RNA and the enzyme reverse transcriptase instead of DNA as their nucleic acid core.

• Once inside the host cell, reverse transcription (making DNA from RNA) is accomplished by the reverse transcriptase, turning the single-stranded RNA into DNA. This new DNA is incorporated into the host DNA, where it transcribes new viral RNA genomes, as well as the RNA to synthesize new reverse transcriptase and protein capsules.

• Viruses are usually quite specific as to their hosts and even to the types of cells they infect in a multicellular host.

• Viruses can NOT be treated with antibiotics because antibiotics are designed to attack the cell wall or membrane and viruses do not have these!

Viroids and Prions

• Viruses would appear to be the simplest form of infectious particle.

• The discovery of viroids, nucleic acid without a protein capsule and prions, infectious proteins, subtracts another level of complexity.

• Both viroids and prions can cause diseases.

Review sheet

1. What is taxonomy?

It is a systematic method of classifying plants and animals.

2. What is binomial nomenclature?

It is a 2 name system so that no two organisms will ever have the same name.

3. Who is the person who came up with the 2 name system?

(Linnaeus)

4. What are the levels of classification from least to most specific?

Kingdom , Phylum (Division for plants) , Class, Order , Family , Genus , Species

5. Name the 6 kingdoms

Archaebacteria, Eubacteria, protist, fungi, plant, animal

6. Are viruses alive? Why or why not?

Viruses are NOT one of the 6 kingdoms and are not considered “alive” because they are not made up of cells, do not metabolize, can only reproduce inside another living cell and do not grow.

7. What is a virus?

A virus is a submicroscopic infectious particle composed of a protein coat and a nucleic acid core.

8. Can viruses be treated with antibiotics?

Viruses can NOT be treated with antibiotics because antibiotics are designed to attack the cell wall or membrane and viruses do not have these!

9. What are the characteristics of the kingdom Archaebacteria?

Prokaryotic, Unicellular, Autotroph/ heterotroph

10. What are examples of A bacteria? Where do you often find them?Three types of Archaebacteria: methanogens, halophiles, and thermacidophiles. They live in extreme habitats like very salty water!

11. Describe EubacteriaProkaryotes, unicellular, autotroph/heterotroph

12. What are the three main shapes of bacteria?

Round, cocci, Rod, bacilli, Spiral, spirilli

13. What is binary fission? Cell division

Why do bacteria use this? Bacteria can reproduce by binary fission

14. Describe the Protist kingdom.

Eukaryotic, unicellular/ some multi, heterotrophic and autotrophic

15. List some examples of protists

Euglena, amoeba, red algae

16. Describe the FUNGI kingdomeukaryotic, multicellular, heterotrophic, chitin in cell walls

17. List some examples of fungi.

Mold, athletes foot, mushrooms