PART 8: Diversity of Organisms1. Phylogeny: the sum of relations between organisms

Taxonomy: the science of classifying organisms according to their phylogeny. Taxonomy is organized into the following classifications:

o Domain: the highest taxonomic rank of organisms, higher than a kingdom.

o Kingdom: subcategory of domaino Phylum: subcategory of kingdomo Class: subcategory of phylumo Order: subcategory of classo Family: subcategory of ordero Genus: subcategory of familyo Species: subcategory of genus

It is beneficial here to make up a word association to remember the order. In Biology 2201, we came up with: Dumb Kim Possible Came Over For Gene Simmons.

2. Binomial (nomenclature) classification: how we name an organism. Organisms are named by their genus followed by their species. For example, the classification of human is:

Domain: eukarya Kingdom: animalia Phylum: chordate Class: mammalia Order: primates Family: hominidae Genus: homo Species: sapiens

Therefore, our binomial nomenclature is: homo sapiens

3. Bacteria: prokaryotic, one-celled organisms that fall under two domains (archaea and bacteria) and under two kingdoms (archaeabacteria and eubacteria).

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4. Domain: a relatively new classification level; there are three domains. Archaea: domain with one kingdom of archaeabacteria Bacteria: domain with one kingdom of eubacteria Eukarya: domain with four kingdoms of protista, fungi, plantae and

Animalia

5. Kingdom: next smallest level of taxonomy with more similar characteristics; there are 6 kingdoms:

Kingdom Archaebacteria: considered extremophiles as they live in extreme environments such as volcanoes and salt lakes. They lack peptitogycan in their cell walls, have unusual fatty acids in the plasma membrane, and animal-like ribosomes.

o Methanogen: convert CO2 and H2 to methane for survivalo Thermophiles: living in extreme hot temperatureso Halophiles: living in salt lakes

Kingdom Eubacteria: “classic” bacteria; single-celled prokaryote lacking a nucleus, having a peptitogycan cell wall.

o Cyanbacteria: phosphosynthetic autotrophso Chemoantotrophs: nitrogen fixingo Decomposition bacteria: break down organic materialo Pathogens: disease-causing parasiteso Cocci: spherical shapedo Bacilli: rod-shapedo Sprilla: corkscrew-shaped

o Obligate aerobes: bacteria that need oxygen to surviveo Obligate anaerobes: bacteria that can’t survive in the presence of

oxygen. They are often found at the bottom of the ocean with sulfur vents.

o Facultative anaerobes: bacteria that can survive with and without the presence of oxygen

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o Legumes: plants with nitrogen-fixing bacteria on their rootso Eubacterial reproduction: as discussed in cellular reproduction,

bacteria divide by binary fission. Although this is asexual, bacteria still share genetic information with each other in three ways...

Transformation: random DNA in the environment is engulfed into the cell

Conjugation: pili (bridges between membranes of two bacterium) are formed to exchange genetic information

Transduction: when viruses unintentionally transfer DNA from one bacteria to another during infection

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Kindgom Fungi: multicellular or unicellular eukaryotes with cell walls made of chitin. Heterotrophic (because they have no chlorophyll) and off organic matter by secreting digestive enzymes from thread-like structures called hyphae. They have parasites, pathogens (athlete’s foot) and decomposers (mushrooms). They reproduce in two ways:

o Spores: minute, typically one-celled, reproductive unit capable of giving rise to a new individual without sexual fusion.

o Budding: a form of asexual reproduction in which a new organism grows on another one. The new organism remains attached as it grows, separating from the parent organism only when it is mature.

Kingdom Protista: multicellular or unicellular eukaryotes. It’s like the “left over” kingdom as it has plant-like, animal-like and fungus-like organisms that did not fit the criteria of plants, animals and fungi.

o Sporophyte: diploid spore-forming structure of the first half of reproduction.

o Gametophyte: haploid gamete-forming structure of the second half of reproduction. Gametophytes are produced by sporophytes, while gameteophytes produce more sporophytes.

o Plant-like protists: protists that are photosynthetic such as: Euglenophyta (fresh water) Dino Flagellata (fresh and salt water) Chrysophyta (golden algae) Chlorophyta (green algae) Phaeophyta (brown algae) Rhodophyta (red algae) Bacillariophyta (non-motile)

o Animal Like protists: non-photosynthetic protists that are heterotrophic, such as:

Zoomastigina (parasites)

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Rhizopoda (amoeba) Ciliophra (paramecium) Sporozoa (spore-forming parasites, ex: plasmodium which

causes malaria) Foraminifera (shelled)

o Fungus-like protists: slime moulds that produce multinucleated (cells with 2 or more nuclei) masses, using spores or gametes. Found in the same places as fungi. Ex: myxomycota.

Kingdom Plantae: multicellular and photosynthetic eukaryotes with cellulose cell walls. All except the first two phyla listed are important to know...

o Sphenophyta: vascular plants (meaning plants that can transport water against gravity with adhesion and cohesion) with scaled leaves and hollow, ribbed stems. Found in marshes.

o Lycophyta: mosses with rhizomes and sort, erect branches.

o Bryophytes: primitive, low growing plants that lack stems, roots and leaves. Root-like structures called rhizoids anchor them to the ground. They self-fertilize as water allows sperm to move from the antheridium (male reproductive part) to the egg in the archeogonium (female reproductive part). Mosses, hornworts and liverworts are all bryophytes.

o Pterophyta (ferns): seedless vascular plants. They have a unique cycle called alternation of generation which very similar to the

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reproductive cycle of protists (sporophytes and gametophytes) with the sporophyto dominating. They reproduce by alternation of generations:

Alternation of Generations

o Coniferophyta: also known as gymnosperms – woody plants that bear their seeds in cones. Most trees are a good example as they don’t need water to fertilize; they are capable of secondary growth (ex., branches) and they have very well-developed vascular tissue (allowing them to grow very tall).

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o Anthophyta: flowering plants with seeds enclosed in a nut or fruit; also known as angiosperms.

o Monocots: angiosperms with flower parts (such as petals) in multiples of three, scattered vascular tissues, a fibrous root system (stringy) and leaves with parallel veins. Monocots also have just one cotyledon (embryonic seed leaf).

o Dicots: angiosperms with flower parts (such as petals) in multiples of four or five, vascular bundles arranged in a circle, a taproot system and leaves with netted veins. Dicots also have two cotyledon.

Kingdom Animalia: continued as Vocab #6 due to length of section.

6. Kingdom Animalia: multi-cellular heterotrophic eukaryotes that are extremely diverse.

Body plan: animals are very diverse in their body plans.o Asymmetry: an animal that has no symmetry (e.g., sponge).o Radial symmetry: circular body pattern (e.g., anemone).

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o Bilateral symmetry: vertically symmetrical; have an anterior (head), posterior (tail), ventral (stomach), and dorsal (back).

o Cephalization: the tendency for sensory (5 senses) and neural (brain) organs to be concentrated in the anterior region of animals with bilateral symmetry.

o Diploblastic: animals with two skin layers; ectoderm (outside) and endoderm (inside).

o Triploblastic: animals with three skin layers; ectoderm (outside), mesoderm (middle), and endoderm (inside).

o Acoelomates: animals lacking true body cavities.o Coelomates: animals with a body cavity derived from the blastocoels.

Phylum of Animalia: there are 10 phyla:o Porifera: sponges, no-motile, diploblastic, radial symmetry,

acoelomateso Cnidaria: cnidarians (ex., jellyfish, anenomes), diploblastic, digestive

cavity, stinging tentacles, acoelomates, radial symmetryo Platyhelminthes: flatworms, motile, bilateral symmetry,

triploblastic, acoelomates, can be parasitic, can regenerate (cut it in half – turns into two worms)

o Nematoda: roundworms, pseudocoelomate, complete digestive tract, some are parasititc.

o Rotifera: tiny filter feeders, pseudocoelomate, complex digestive system

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o Mollusca: molluscs, motile, soft body with hard shell, coelomate, octopus/squid/snail/clam

o Annelids: segmented warm with mouth and anus, developed digestive circulatory, and nervous system, short appendages (e.g., earthworms)

o Arthropoda: animals with segmented bodies, paired and jointed legs, chitin exoskeleton, dorsal heart and open circulatory system (e.g., insects, crustaceans, arachnids [spiders])

o Echinodermata: non-motile, spiny exoskeleton, deuterosomes (e.g., sea urchin)

o Chordata: Vocab #7 because of length.

7. Chordata: phylum of Kingdom Animalia. Animals with a notochord, a dorsal nerve, a post-anal tail, and with gills at some point in life. Most are vertebrates (with bones in the back), although there are a few invertebrates (no bones in the back). The classes of chordata are:

Pisces: fish, cold-blooded, vertebrates, gills, scales, two-chambered heart, external fertilization.

Amphibia: gills and lungs (can live in water or on land), can exchange gases through the skin, have a three-chambered heart (e.g., frogs), external fertilization.

Reptilia: cold-blooded, chitin covered eggs, four-chambered heart, internal fertilization.

Aves: birds, warm-blooded, shelled eggs, internal fertilization, wings, feathers, hollow bones, four-chambered heart.

Mammalia: warm-blooded, four-chambered heart, produce milk (females) to feed offspring.

o Placental mammals: mammals that develop a placenta (pouch that nourishes the fetus in the uterus during embryonic development).

o Non-placental mammals: mammals that do not develop a placenta; also known as marsupials. The fetus only matures in the uterus to about 8 days, when it is then moved to the mother’s pouch to finish growing.

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8. Viruses: organisms that are not definitively “alive”, although they do reproduce by infecting living cells. A virus is made up on only a protein coat and a viral chromosome of either DNA or RNA.

Structure: viruses can be found in these structures:

Lysis (Lytic Cycle): the reproductive cycle of a virus. A virus attaches to a living cell (host cell) and injects its viral chromosome into the host cell. The viral nucleic acid takes over the cell’s organelles until the host cell has produced viral components. The components form new viruses which then burst out of the host cell, killing it.

Lysogenic Cycle: when viral DNA inserted by the virus integrates into the host cell’s DNA. Here the viral genes can lay dormant (not producing virus components) as a temperate virus. Eventually, the cell will revert back into the lytic cycle, killing the host cell. Basically, it is a less aggressive virus as it takes longer to spread.

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Retrovirus: when viral RNA inserted in the virus integrates into the host cell’s DNA, that virus was a retrovirus. In order for the viral RNA’s sequence to bind to the DNA, it must be translated. An enzyme called reverse transcriptase completes that task, creating a viral DNA from the RNA so that it can attach. This enzyme is either brought by the virus or translated on a ribosome by the viral RNA. Because this work is opposite to all other genetic reproduction (RNA – DNA rather than the usual DNA – DNA/RNA), it has deadly consequences and is hard to cure. HIV (virus that leads to AIDS) is a retrovirus and so are many cancer-causing viruses.

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