Classification and the 6 kingdoms I Taxonomy Classification

Classification and the 6 kingdoms

I. Taxonomy (Classification) is the branch of biology concerned with: A. Reconstructing phylogeny (evolutionary history) B. Naming organisms and placing them into hierarchical categories based upon their evolutionary relationships C. The eight major categories of classification, in order of decreasing inclusiveness are: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Classification of the diversity of species is studied by: a) evolutionists b) taxonomists c) theorists d) taxidermists

II. History of Taxonomy – Aristotle’s System (more than 2, 000 years ago) 1. He classified all living things known at that time into two major groups—plants and animals. 2. He grouped plants and animals according to their structural characteristics. 3. Plants were classified as trees, shrubs, and flowers. 4. Animals were grouped according to where they lived— on land, water, or air. 5. Later observations convinced scientists that Aristotle’s system did not work. They observed that some animals, such as frogs, lived both on land in water. Scientists also realized that Aristotle’s classification system did not show natural relationships among organisms.

Aristotle

B. Carolus Linnaeus 1. An 18 th century Swedish botanist developed a method of classification that is still used today, which is called binomial nomenclature. 2. Binomial nomenclature is a system by which each species is given a 2 word Latin name. 3. Linnaeus selected physical characteristics that led to classification based on close relationships of organisms. 4. Example for plants: He based his classification of flowering plants on the numbers and similarities of their reproductive structures. 5. Example for animals: He selected characteristics of organisms that also led eventually to classifications based on evolutionary relationships.

6. Linaeus’ system uses 2 scientific names: a. The first part of the name is the genus— genus refers to the relatively small group of organisms to which a particular type of organism belongs. b. The second part of the name is the species- This is usually a description of some important characteristic. Example: Red Maple—common name Acer rubrum—scientific name (genus) (species)

C. Before 1969, all forms of life were classified into two kingdoms 1. Animalia 2. Plantae (included plants, bacteria, fungi and photosynthetic eukaryotes) D. Proposed by Robert H. Whittaker (1969) Kingdoms include: 1. Monera (all prokaryotes) 2. Plantae 3. Fungi 4. Animalia 5. Protista (eukaryotes that are not plants, fungi, or animals)

III. Scientific Names A. Common names are everyday names given to organisms. Common names may not accurately describe an organism. Example: Jellyfish is not a fish…but a Cnidarian. B. A scientific name is composed of the genus and the species. C. There are 3 rules to follow when writing scientific names: 1. Always capitalize the genus name. 2. Always leave the species in lowercase. 3. Always underline both names (unless typing. . . then use italics). Example: Home sapiens—Humans or if typing, Home sapiens Felis domesticus—Cat Canis familiaris—Dog Rana pipiens—Frog

D. Trinomial nomenclature - when organisms can be divided even further into subspecies or varieties. Used when three scientific names are given. Ex: Acer rubrum var. drummondii is a Drummond’s red maple. Acer is the genus, rubrum is the species and drummondii is the variety of red maple that grows in the coastal plains area.

IV. Classification system of organisms from largest to smallest: This is the system most scientists use that puts each living thing into groups, organized from the most general to the most specific. Therefore, each species belongs to a genus, each genus belongs to a family, and each family belongs to an order. These are hierarchies. A. Domain: : Eukaryotic/Prokarytoic B. Kingdom: In the kingdoms, there are huge groups, encompassing millions of kinds of organisms in each. This group has the most, and as you go down, the number of different kinds of organisms decrease. In other words, the more specific it becomes.

C. Phylum or Division: A group of related classes. 1. Animal groups are called phyla. 2. Plant groups are called division. 3. All of the animals in the phylum vertebrata must belong to the same kingdom. 4. Chordata is to Animalia as phylum is to Kingdom. D. Class: A group of related orders. E. Order: A group of related families. F. Family: A group of closely related genera G. Genus: A group of similar species that are alike in general features and are closely related is a genus. Example: The leopard frog is know by the scientific name Rana pipiens. The wood frog is known as Rana sylvatica. What is the smallest classification division these frogs have in common? genus

H. Species: Species are the _most specific. A species consists of all the animals of the same type, who are able to breed and produce young of the same kind. 1. This biological classification group has the fewest members. 2. Organisms that look alike and successfully reproduce fertile offspring belong to the same species. 2 organisms would be most closely related if they are classified in the same species. 3. Ex: 2 plants probably belong to the same species if they can producefertile offspring.

4. The biological species concept defines species as “groups of interbreeding natural populations, which are reproductively isolated from other such groups” -Cannot be applied to asexually reproducing organisms 5. Alternative species definitions have been proposed, one of which is the phylogenetic species concept a. The phylogenic species concept defines a species as “the smallest diagnosable group that contains all the descendants of a single common ancestor” b. Can be applied to sexually and asexually reproducing organisms c. May eventually replace the biological species concept

I. The more categories two organisms share, the closer their evolutionary relationship J. Today, scientists classify organisms according to the 1. Evolutionary history of the species. 2. The external and internal characteristics of organisms and 3. Chemical makeup—DNA (the genetic material). This is the best way to determine any taxonomic relationship between 2 organisms.

A group of related organisms that are able to interbreed in nature & produce fertile offspring is a: a) species b) phylum c) genus d) order

The taxonomic group that shows the greatest similarity among its members is the: a) kingdom b) class c) species d) family

Which statement describes organisms that are classified in the same genus? a) They must be in the same phylum, but may be of a different species. b) They must be of the same species, but may be in different phyla. c) They must be in the same kingdom, but may be in different phyla. d) They must be in the same class, but may be in different phyla.

As we move through the taxonomic groups from the kingdom to the species level, organisms: a) become more similar in appearance b) vary more & more c) are less related to each other

Which of these taxonomic classification groups has the fewest members? a) species b) family c) class d) genus

• • Classification of Humans: Kingdom: Animalia Phylum: Chordata Class : Mammalia Order: Primate Family: Hominidae Genus: Homo Species: sapiens

Spurge Cactus

V. Taxonomy Reveals Evolutionary History A. Linnaeus’s classification system was based on the fact that organisms have different degrees of similarities. Ex: Tigers resemble gorillas more closely than they resemble fish. B. According to Darwin’s views, organisms that are similar descended from a common ancestor; therefore, classification provides strong evidence of evolution.

C. Making evolutionary connections based on similar traits can be misleading because not all traits are inherited from a common ancestor. Ex: The wings of a bird and the wings of an insect. Both enable flight, but the two kinds of wings are built differently, and based on fossil evidence, we know they evolved independently of each other. D. Convergent evolution is when organisms evolve similar features independently, often because they live in similar habitats. 1. Convergent evolution is the process by which unrelated species become similar as they adapt to similar environments. Similar features that evolved through convergent evolution are called analogous structures or homoplasies. 2. Ex: Although they evolved in differently whales on land fish in water, whales and fish have similar structures.

The scientific name for the fruit fly is Drosophila melanogaster. The word Drosophila refers to the taxonomic group: a) kingdom b) genus c) species d) phylum

Scientists use a 2 -name method of providing scientific names to organisms that is called: a) binomial nomenclature b) scientific nomenclature c) theoretical nomenclature

The scientific name of an organism: a) varies according to the native language of scientists. b) is the same for scientists all over the world. c) may refer to more than 1 species. d) is different for scientist all over the world.

The language of scientific names is: a) English b) Latin c) Spanish d) French

Of the following, Felis leo, is most closely related to: a) Rana pipiens b) Xenopus laevis c) Felis domesticus d) Elephas maximus

Scientific names come from the taxonomic groups: a) kingdom & phylum b) class & family c) genus & species d) order & family

E. Unique characteristics help distinguish groups: 1. Modern taxonomists use the phylogeny (evolutionary history) of an organism to classify it. 2. A phylogenetic tree is a family tree that shows the evolutionary relationship thought to exist among groups of organisms. Scientists construct a phylogenetic tree by using several lines of evidence such as: a. fossil records b. An organism’s morphology compared to the morphology of other living things c. Embryological patterns of development d. Comparisons of macromolecules such as DNA, RNA, and proteins as well as an organism’s biochemistry.

F. Cladistic taxonomists use derived characters to establish evolutionary relationships 1. Derived characteristic -feature that evolved only within the group under consideration. 2. Example: a derived character for birds is feathers.

The red maple tree is known by the scientific name Acer rubrum. The sugar maple tree is known as Acer saccharum. What is the smallest classification division these trees have in common? a) phylum b) order c) genus d) species

It is easy to group snakes based on color. However, a scientist would prefer a system that shows how snakes: a) get their food b) shed their skin c) are genetically related d) mate

G. Many taxonomists give varying degrees of importance to characters and thus produce a subjective analysis of evolutionary relationships called evolutionary systematics. 1. Evolutionary systematics is the approach of choice when a great deal of information about a group of organisms is available. When little information is available about how a character affects the life of an organism, cladistics is the better choice. 2. Ex: Evolutionary systematics places birds in an entirely separate class from reptiles, which gives more importance to characters like feathers that made powered-flight possible. H. Dichotomous keys: tool used by scientists to classify organisms, using a system of questions. Ex:

VI. Biodiversity A. The total number of species in an ecosystem B. Number of named species is currently about 1. 5 million (biased toward large organisms in temperate regions) a. 5% prokaryotes and protists b. 22% plants & fungi c. 73% animals C. Estimated that 7 million to 10 million species may exist D. Between 7, 000 and 10, 000 new species are identified annually, mostly in the tropics E. Tropical rain forests are believed to be home to 2/3 of the world’s existing species, most of which have yet to be named F. Because tropical rain forests are being destroyed so rapidly, species may become extinct before we ever knew they existed

There is a six-kingdom classification system: 1. Kingdom Archeabacteria 2. Kingdom Eubacteria 3. Kingdom Protista 4. Kingdom Fungi 5. Kingdom Plantae 6. Kingdom Animalia Kingdoms 1 and 2 used to be combined into Kingdom Monera

I. Both Archaebacteria and Eubacteria: (_MONERANS) A. Both are prokaryotes—_DO NOT HAVE A NUCLEUS OR MEMBRANE BOUND ORGANELLES B. Small (microscopic), simple, and lack membrane-bound organelles. C. DNA is found _FLOATING IN THE CYTOPLASM_. D. Most _UNICELLULAR_ (1 cell) E. Most numerous and widespread organisms on the earth

F. Both reproduce by _BINARY FISSION_. 1. The cell pinches into 2 cells, 2. a form of asexual reproduction that produces identical offspring. 3. In asexual reproduction, a single parent passes exact copies of its entire DNA to its offspring. 4. Binary fission can occur every 20 minutes 5. Rapid reproductive rate allows for rapid evolution 6. Mutations in DNA replication are rapidly spread

G. Bacteria use _CILLIA_ and _FLAGELLA_ to aid in movement 1. In bacteria, a "wheel-and-axle" arrangement anchors the flagellum within the cell wall and plasma membrane, enabling the flagellum to rotate rapidly H. Bacteria can have _PILI_, which enable bacteria to attach to surfaces or to other cells. I. Both are _MICROSCOPIC _ and _PROKARYOTIC_.

J. Metabolism in Bacteria 1. Anaerobic Metabolism a. Some bacteria live without oxygen (and are poisoned by it) e. g. Tetanus bacteria 2. Some bacteria can switch between aerobic and anaerobic respiration e. g. Escherichia coli in our large intestines 3. Bacteria Food: a. Familiar organic compounds such as sugars, carbohydrates, fats, and proteins b. Compounds poisonous to humans such as petroleum, methane, benzene, toluene c. Inorganic molecules such as hydrogen, sulfur, ammonia, iron, nitrite

d. Sunlight such as: 1. Cyanobacteria perform photosynthesis 2. Sulfur bacteria use H 2 S instead of water in photosynthesis K. Some bacteria secrete sticky layers of polysaccharide or protein slime 1. Aggregates (communities) of slimesecreting bacteria are called biofilms 2. Dental plaque is a biofilm 3. Bacteria embedded in biofilms are protected from disinfectants and antibiotics

II. The Structure of Monerans A. 3 Main Shapes of Bacteria (Monerans): Examples: 1. Ball-shaped (_COCCI)--Staphlococci mutans which Causes tooth decay. 2. Rod-shaped (BACILLI)--E. coli and Clostridium botulinum which causes food poisoning. 3. Corkscrew-shaped (_SPIRILIA)-Treponema pallidum which causes Syphillis

B. Bacterial Cells are also classified by their arrangement: 1. DIPLO_refers to cells that are paired 2. STAPHYLO_ refers to cells arranged in grapelike clusters. 3. STREPTO refers to cells arranged by long chains.

III. Classification of Bacteria A. Features used in prokaryotic classification: 1. Shape 2. Means of locomotion 3. Pigments 4. Nutrient requirements 5. Colony appearance 6. Gram staining characteristics 7. Nucleotide sequences B. The kingdom used to be referred to as the kingdom MONERA (bacteria), which now is divided into Archaebacteria and Eubacteria probably diverged from each other several billion years ago.

C. _ARCHAEBACTERIA_ 1. They are the earliest monerans (prokaryotes or bacteria). 2. The cell walls of Archaebacteria do NOT contain PEPTIDOGLYCAN_. 3. Their relationship to each other is shown through their RNA sequencing.

4. There at least three major groups of socalled “extremophile” Archaebacteria, each living in very different hostile environments. a. _METHANOGENS_ obtain their energy by making methane gas (CH 4) from other organic compounds. They are found in swamps. b. _THERMOPHILES live in very hot water (140º F – 176º F), such as the water near deep sea hydrothermal vents. Some obtain their energy from sulfur. c. HALOPHILES_ live in very salty places, like the Great Salt Lake, in Utah.

Halophiles Methanogens Thermophiles

Kingdoms Archaebacteria and Eubacteria are sometimes referred to asa) Kingdom Arachaialeu b) Kingdom Euarchae c) Kingdom Monera d) Kingdom Protista

All bacteria: a) cause disease b) lack a nucleus c) are autotrophic d) contain a nucleus

D. EUBACTERIA_ 1. Eubacteria have strong exterior cell walls made of _PEPTIDOGLYCAN. 2. Eubacteria are found in practically every environment on earth, and they have an impact on humans every day. Some normally live in and on your _BODY_. Some Eubacteria cause _DISEASES_. Other Eubacteria are used by humans to process foods, to control agricultural pests, to produce various chemicals, and to use in genetic engineering.

a. Some eubacteria obtain energy from inorganic compounds such as hydrogen sulfide, ammonia, and methane. b. Some are photosynthetic and are found in ocean and freshwater environments, where they are producers. c. Some are heterotrophs and are capable of living in the absence of oxygen (__ANAEROBIC) while others must have oxygen (_AEROBIC_) to live.

IV. Bacteria and Human Life A. Most bacteria are important and beneficial to life. Some are harmful and produce endospores which can cause botulism or tetanus. Others cause Lyme disease, strep throat, and cavities in your teeth B. Benefits to Human Life 1. Roots of certain plants. a. Nitrogen-fixing bacteria are an important part of the nitrogen cycle, live in the soil help to break down and recycle organic and inorganic materials and put oxygen back in the atmosphere. b. Many foods such as pickles, yogurt, sauerkraut, and swiss cheese depend on bacteria for their distinctive odors and flavors.

2. Medicine and Human Health a. Certain kinds of bacteria are used to make antibiotics, such as neomycin and erythromycin, which are used to destroy other bacteria. b. Bacteria called probiotics are important for human health. They live in the intestines and produce certain vitamins, enhance the absorption of nutrients, and strengthen the immune system. c. Create environment hostile to pathogenic infection in vaginal tract d. Produce vitamin K in our intestines

3. Animal Metabolism a. Leaf-eating animals (ruminants) depend on bacteria to break down cellulose (e. g. rabbits, cattle) b. These animals couldn’t live without this bacteria 4. Pollution a. Nearly all human-made substances are biodegradable by some bacterial species b. Oil-eating bacteria were used in clean up of Exxon Valdez oil-spill disaster c. Some sewage treatment plants use bacteria to clean sewage

C. Harmful to Human Life 1. Endospores a. Form inside some bacteria under inhospitable environmental conditions b. Endospores are thickly-wrapped particles of genetic material and a few enzymes c. Endospores are resistant to extremes 1. Survival in boiling water, why is this bad? ? 2. Stable and long-lived (> 250 million years) 3. Ideal bioterror agent (e. g. anthrax spores)

Endospore

2. Poisons a. Some anaerobic bacteria produce dangerous poisons: 1. Clostridium tetani causes tetanus 2. Enters body through puncture wound 3. Produces paralyzing poison b. Clostridium botulinum causes botulism 1. Reproduces in under-sterilized canned food 2. Botulism toxin is very potent 3. Honey can produce botulism in infants because their digestive system is too immature to handle it

Tetnus

3. Disease a. Bubonic Plague (Black Death) 1. Caused by Yersinia pestis and spread by rat fleas 2. Killed 100 million people in the 1300 s b. Lyme Disease (emerged in 1975) 1. Caused by spiral-shaped Borrelia burgdorferi 2. Carried by deer ticks which bite humans 3. Flu-like symptoms can lead to arthritis and heart and nervous system problems c. Other historical bacterial diseases disappear and then reoccur 1. Tuberculosis (once thought to be vanquished from the United States) 2. Gonorrhea and syphilis (sexually transmitted) 3. Cholera (water-transmitted in contaminated drinking water)

Botulism

Bubonic Plague

Lyme Disease syphilis

d. Common Diseases 1. Streptococcus bacteria may cause strep throat, pneumonia, or necrotizing fasciitis (flesh-eating bacteria) 2. Escherichia coli a. Common inhabitants of digestive system b. O 157: H 7 E. coli strain is pathogenic 1. Transmitted through undercooked hamburger 2. Causes intestinal bleeding and can be fatal

D. _ANTIBIOTICS_ 1. Chemicals that are capable of inhibiting (killing) the growth of some bacteria. 2. _KILLS OR WEAKENS_ any organism that causes a disease. 3. The first antibiotic was _PENICILLIN_, made by the fungus Penicillium, and was discovered by _ALEXANDER FLEMING_. 4. Many pathogenic bacteria have become _RESISTANT_to antibiotics. At first, a population of bacteria will die when exposed to an antibiotic. But some may have mutations and be able to survive. When those reproduce, they pass their resistance on to their offspring. 5. Antibiotics would only be effective against bacterial infections: antibiotics _DO NOT_ affect viral infections. 6. In other words, ANTIBIOTICS KILL BACTERIA. ANTIBIOTICS DO NOT KILL VIRUSES.

II. Viruses A. Do not belong to a kingdom because they are not considered to be LIVING organisms B. Examples of Viruses: flu, chicken pox, HIV, cold sores, and some can cause cancer C. The biggest viruses are 1/100 the size of prokaryotic cells (bacteria/without a nucleus or membrane bound organelles). Most bacteria are even smaller than half the size of a prokaryotic cell.

D. Considered to be non-living because they CAN”T : 1. Grow 2. Develop 3. Obtain energy 4. Reproduce on their OWN; viruses must use a HOST cell to reproduce

E. Virus classification or names come from: 1. The TYPE OF CELLS they affect; ex: adenovirus affects the adenoids in the throat 2. The DISEASES they cause; Ex: poliovirus causes polio 3. Some of the viruses are similar and are therefore given a number as part of their name 4. BACTERIOPHAGES are viruses that affect bacteria

F. Virus Structure 1. Contain an inner core of NUCLEIC ACIDS a. Viruses either have DNA or RNA but NEVER both 2. CAPSID : protein coat that surrounds the nucleic acid; the way the proteins are arranged determines: a. The SHAPE of the virus b. The cells the virus can affect c. The WAY the virus infects the cells 3. ENVELOPE: Some, but not all, viruses have an envelope that acts like a plasma membrane

G. LYTIC Cycle (Virus Reproduction) 1. Viruses take over the genes of the host cell 2. They use the genes to make more viral genes and viral protein 3. This continues until the cell is so full of viruses it actually BURSTS intern killing the host cell and releasing more viruses into the body 4. Viruses can infect: a. PLANTS b. animals c. bacteria

Cluster of Flu Viruses Common Plant Virus

5. The only way a virus can infect a living cell is if a receptor site on the host cell MATCHES that of the virus. a. Specific cells are only vulnerable to certain VIRUSES b. Ex: Tobacco mosaic virus can only invade the leaves cells in a tobacco plant (The reasons dogs don’t catch your colds) 6. Antibiotic DO NOT kill VIRUSES because Anti means against and bio means life so against life…viruses are non-living, you can’t kill something that isn’t alive

H. Virus Types: 1. Virus can be either _DNA_ viruses or _RNA_ viruses 2. DNA virus-do one of the following: a. Directly produce viral _GENES_ that makes more viral proteins and parts. b. Join to the host cell’s DNA to direct synthesis of new viruses. 3. RNA virus-does one of the following: Protein Coat(Capsid) a. Some RNA viruses enter the cell and use the host’s ribosomes to produce new viral proteins EX: polio virus b. Some RNA viruses are _RETROVIRUSES__. They use an enzyme, called reverse transcriptase, which uses viral RNA as a template to make viral DNA. The DNA is integrated into the hosts cell’s DNA. Then, the viral DNA makes viral RNA, which translates into viral proteins. EX: _HIV_

: Chicken pox

Warts

Common cold

Mumps

Small pox

Influenza (flu)

Mononucleosis

AIDS

Antibiotics would be effective against- a) bacterial pneumonia b) the malarian protist c) flu virus d) viral meningitis

Which characteristic do viruses posses in common with living cells? a) They contain a nucleus & organelles b) They make their own food. c) They contain nucleic acids, such as DNA or RNA. d) They are given scientific names.