Bio Exam Prep U1 PDF

Unit 1: Diversity of Things Science of Classification ​ The names given to organisms often reveal: ​ The evolutionary history of their species ​ Ecological relationships with other species ​ Distinguishing characteristics of that species Taxonomy is the science of...

Unit 1: Diversity of Things Science of Classification ​ The names given to organisms often reveal: ​ The evolutionary history of their species ​ Ecological relationships with other species ​ Distinguishing characteristics of that species Taxonomy is the science of naming, identifying, and classifying species. Classifying must go beyond physical appearance of organisms. The biological concept of species is “a population of organisms that can breed freely in nature and produce fertile offspring.” The biological concept of species does not work for all species. Carolus Linneaus devised the binomial nomenclature system for classification in the 1750s. A two-part (= binomial) Latin name (= nomenclature) for each species (Genus and species) Names written in italics (Homo sapiens, or H. sapiens) Genus first letter is CAPITALIZED, species lowercase Each category level is called a taxon (plural, taxa). From broadest to most specific, taxa are: kingdom, phylum (plural, phyla), class, order, family, genus (plural, genera), and species. Acronym: King Phillip Came Over For Ginger Snaps Modern classification does not use morphology as much as the Linnean classification system. Morphology is the study of the form and structure of organisms. Problems arise in situations like the koala, giant panda, and polar bears, which look alike, but have major differences. Charles Darwin and the theory of evolution promoted classification based on evolutionary relationships. Classification by phylogeny uses e0volutionary relationships. Classification within taxa is based on common ancestors. Classification by evolution used several types of evidence. Fossils and molecular analysis are the best evidence. Closely-related species have similar proteins and DNA. Morphology and physiology often must be used as well. Phylogenetic trees show the evolutionary relationships between taxa. Branches reveal evolutionary relationships, with species on tips. Nodes represent common ancestors or descendent taxa. The more branching there is, the more evolution and speciation has occurred. The further from the tips, the older (more evolved) the phylogenetic relationships. These trees are very useful when closely-related species are considered. There are considered to be three domains in phylogeny. These are now the broadest taxa. The three domains are Bacteria, Archaea, and Eukarya. Bacteria and archaea are microscopic, unicellular, and have no nucleus or other membrane-bound organelles. Bacteria and archaea are prokaryotic (no nucleus) organisms. All other organisms are in the domain Eukarya. All have eukaryotic cells (nucleus and membrane-bound organelles) Viruses & Prokaryotes Viruses are not considered to be living organisms. However, they do have DNA and RNA, and can adapt to change. They are made of proteins and nucleic acids, not cells. They must use a host cell to reproduce. The structure of a virus is well-suited to its function of entering a host cell and reproducing. Viruses come in many shapes and sizes. They are usually classified by the type of cell they infect. Their protein coat is like the key to a specific cell membrane, e.g., HIV only infects T cells of the immune system. Sometimes, such as the avian flu virus, the protein coat is a master key. Bacteriophages enter and infect bacteria, and scientists use this fact in biotechnology and gene therapy. Viruses reproduce after infecting a host cell. Lytic cycle: The virus unloads its genetic material, takes control of the cell, replicates necessary virus materials (DNA and proteins), and causes the cell to lyse (burst) and release new viruses. Lysogenic cycle: Viral genes are incorporated into host cell’s DNA, host cell reproduces normally, an environmental change triggers the virus to separate from host DNA, and the viral DNA in each host cell (old and new) enter the lytic cycle. In the three-domain system, two domains are prokaryotes (Bacteria and Archaea). Prokaryotes have no nucleus or membrane-bound organelles. The third domain is Eukarya. Before 1977, all known prokaryotes were bacteria. Woese discovered organisms that looked like bacteria, but acted like eukaryotes = the domain Archaea. Archaea means “ancient” in Greek , but organisms in Archaea are actually more complex than bacteria. Organisms in Archaea often live in extreme environments. For this reason, it is thought Archaea might represent the earliest forms of life on Earth. Bacteria exist in very large numbers almost everywhere on Earth. Fresh water can have a million bacteria per milliltre, and some soils can have more than a billion bacteria per gram. Your body has 10 times more bacteria cells than human cells! Some bacteria are harmful, and some are helpful. One type of bacteria might be helpful in one place, but harmful in another (E. coli live in your colon, but also are toxic when ingested). E. coli in the human colon are in a symbiotic relationship. Bacteria cycle nutrients like carbon and nitrogen. Cyanobacteria are very important producers in many water ecosystems. Bacteria are the smallest living cells and require high magnification to be seen. Bacteria are classified by their shape, cell walls, and motility. 1.​ Shapes Spherical: a.k.a. coccus (berry); plural, cocci Pneumonia-causing bacteria are an example. Cocci appear in clusters (Staphlococcus) or chains (Streptococcus). Rod-shaped: a.k.a. bacillus (stick); plural bacilli E. coli are an example. Spiral: curved or spiral-shaped The largest are called spirochetes (long hair). Bacteria that cause Lyme disease are an example. 2.​ Cell wall structure Nearly all bacteria have cell walls outside their plasma membrane, but they are very different from plant cell walls. Type 1: Composed of peptidoglycan (thick coat of sugars) Type 2: Thin coat of peptidoglycan, plus extra membrane 3.​ Movement About half of all bacteria cannot move on their own. Methods of bacterial movement include: Flagellum (plural flagella)--whip-like tail (most common form of bacteria movement) Spiral bacteria twist like a corkscrew. Some bacteria glide on a film of slime. Bacteria obtain their nutrition in a variety of ways: Heterotrophs eat and autotrophs get energy from the Sun or other inorganic source, photo = light. Heterotrophs take up organic molecules from the environment or eat other organisms for nutrition and energy. Photoautotrophs use sunlight and carbon dioxide for energy and to form carbon compounds like sugars. Photoheterotroph use light for energy, but also eat other organisms to get carbon. Chemoheterotroph use chemical reactions for energy source, but also eat other organisms to get carbon. Usually found in dark, chemically harsh locations Bacteria reproduce by binary fission. One original cell splits into two. This can occur in as little as 20 minutes for many bacteria species. In 12 hours, a single bacterium can divide to form a colony of 68 billion cells. Limiting factors, like overcrowding, waste, and food availability do not allow populations to grow this large. Binary fission produces colonies of bacteria that are genetically identical. To increase genetic diversity, bacteria undergo transformation, conjugation, or transduction. Transformation: bacteria pick up stray DNA from their surroundings. Conjugation: two bacterial cells join (= conjugate) to exchange genetic material (plasmids, separate from main DNA) Transduction: viruses that infect bacteria transmit genetic material from another source Endospores form when environmental conditions make normal functions too difficult. A small amount of cytoplasm and DNA form a tough capsule. Prokaryotes can be sensitive to changes in the temperature, pH, or salinity of their environment. Rising ocean levels push salt water into coastal marshes, harming prokaryotes that maintain wetland ecosystems. Methane-producing bacteria help to maintain the ecosystem. Salty conditions favour sulphate-producing bacteria that kill plants. This destroys the peat, and an entire wetlands ecosystem can be lost as a result. Large amounts of CO2 and methane are released, contributing more to global warming and climate change. Fungi Many people think that fungi are a type of plant. Analysis of fungi reveals they are more closely related to animals--even humans--than they are to plants. Fungi are heterotrophic, not photoautotrophic. They release powerful enzymes to break down organic matter, and they require oxygen to survive. There are more than 100 000 known species of fungi. Some of the most common varieties include mushrooms, moulds, mildew, yeasts, truffles, and rusts (not the rust that appears on metal objects). Many fungi play an important role as decomposers. Like some bacteria, fungi can be involved in the cycling of nutrients like nitrogen and carbon. Common homes for fungi include dead and decaying organisms, as well as wastes. Plants require the nutrients cycled by fungi. Four out of every five plants have a symbiotic relationship with some species of fungi. Some species of fungi are parasitic. 80 percent of all plant diseases are caused by fungi. This includes rust, rot, and blight. Humans suffer from fungal diseases like ringworm and athlete’s foot. Fungi have body structures unlike all other eukaryotes. The bodies of most fungi are made up of hyphae. Hyphae are thin threads of cytoplasm, covered by a plasma membrane and a unique cell wall structure. Cross-walls in hyphae make fungi multicellular. Cytoplasm, and organelles, can move through cross walls. Hyphae form a “web” called a mycelium (pl. mycelia) A mushroom is the fruiting body of a fungus, an above-ground extension of the mycelium. The mycelium is the feeding structure. It grows large very quickly. Mycelia underground form a vast network, often working with plant roots as mycorrhizae in a symbiotic relationship. All fungi can reproduce asexually. New fungi can grow from a broken piece of hyphae, or from spores (tough, haploid cells dispersed for reproduction). Many species can also reproduce sexually. Their two sexes are “+” and “–”. Opposite sexes of hyphae fuse to form a diploid zygospore. The zygospore produces haploid spores, which are genetically unique, increasing genetic diversity.  Climate change and fungi Changing temperatures also change the long-term climate, as well as habitats of various organisms. Changing habitats do not affect plants as much as fungi, as plants disperse their seeds very efficiently. Without plants, many species of fungi lose their symbiotic partner. Similarly, when the plants begin to grow in their new location, the symbiotic mycorrhizae may not be present. Air pollution is also destroying many mycorrhizae. The effect on soil ecosystems is unknown. Plants ​ Plants are at the foundation of most non-extreme ecosystems. ​ Plants are at the start of most food chains, converting solar energy to chemical energy, cycling carbon in CO2 into sugars, and removing toxins from soil.(photosynthesis) ​ The Indian mustard plant removes toxic metals like lead, chromium, cadmium, nickel, zinc, copper, and selenium from contaminated soil. ​ We use plants for food, shelter, fuel, fibre, and medicines. ​ Aspirin, quinine (for malaria), and morphine are three medicines derived from plants. ​ As a group, plants (kingdom: Plantae) are very diverse. ​ Plants include trees, wildflowers, mosses, and ferns. ​ Most plants grow on the land, and require optimal amounts of water, minerals, nutrients, soil, sunlight, warmth, and gases. ​ All plants have 3 things in common: 1.​ Plants are eukaryotic. 2.​ Plants have cell walls made of the carbohydrate cellulose. 3.​ Plants use the pigment chlorophyll, found in organelles called chloroplasts, for photosynthesis. ​ Ancestors of modern plants were aquatic organisms similar to green algae. ​ To become land-based, plants developed several adaptations: ​ formation of an embryo that grows into a plant ​ adaptations to absorb sunlight by growing tall or wide ​ tissues to transport nutrients, water, and wastes (xylem/phloem) ​ adaptations to reduce water loss (waxy cuticle) ​ strategies to disperse reproductive structures  ​ Most plants have a life cycle that alternates between haploid and diploid. ​ Diploid = two identical sets of chromosomes, one from each parent. Haploid = one set of chromosomes. ​ Both haploid and diploid forms are multicellular. ​ Sometimes, the haploid version is larger than the diploid. ​ The haploid generation, the gametophyte, produces gametes ​ (-phyte is Greek for “plant”). ​ The diploid generation, the sporophyte, produces spores. ​ A plant’s life cycle is called an alternation of generations if it cycles from one type of generation to the other. ​ In humans, the haploid stage is the sex cells (sperm & egg), whereas normal body cells are diploid. (Eg. Skin cells) There are five major groups of plants on Earth today:  1.​ Green algae are the closest living relatives of ancient plants. ​ Not in the kingdom Protista because of cell walls, photosynthetic pigments, and similarities to plants. 2. Mosses and relatives are seedless, non-vascular plants. 1.​ A.k.a. bryophytes, these were the first land plants to evolve. 2.​ They are short, grow in damp conditions, and have no seeds, stems, or any rigid support structures. 3.​ Non-vascular = no special tissues for moving water upwards. 4.​ Gametophyte is the dominant generation (unique in plants). 3. Ferns and relatives are seedless, vascular plants, that can grow tall. Vascular plants have tissues to carry water upwards, against gravity = vascularization. ​ Phyla include ferns, club mosses, and horsetails. ​ A.k.a. pteridophytes, reproduce similar to mosses; underside of gametophyte produces eggs and flagellated sperm ​ Sporophyte is the dominant generation; brown dots on underside of sporophyte are full of haploid spore capsules. ​ Haploid spores are released from these capsules. ​ When they land on the ground, a new gametophyte grows. 4. Seed plants (gymnosperms) are “naked” seeds, not protected in an ovary. ○​ Examples include conifers like pine, fir, spruce, redwood, and cedar trees. ​ Vascular plants represent the next step in plant evolution. ○​ Seeds = plant embryo + food + protection ○​ Smaller gametophytes than ferns; the sporophyte is the tree, the gametophytes are hidden in the cones ○​ Seed plants use pollen (male gametophytes) to be dispersed by wind (= dry environment), and fertilize female cones, where the female gametophyte is hidden. 5. Flowering plants (angiosperms) were the last major group of plants to evolve; their appearance coincided with the appearance of mammals. ​ Both angiosperms and mammals evolved to conserve water and reproduce effectively on land. ​ Angiosperm = enclosed seed (within the ovary in the flower) so the gametophytes develop within the flower structure. ​ Flowers are most effective reproductive and seed dispersal system in the kingdom Plantae. ​ Flowers often pollinated by animals (also wind) ​ Pollinated flowers = ripened ovary = fruit ​ Transpiration is the release of water through the leaves. ○​ This pulls water upward from the ground, so photosynthesis can occur in  the leaves. ​ Transpiration is responsible for the release of large amounts of water vapour into the atmosphere. ​ Removal of plant life, especially forests, can change rainfall patterns due to loss of transpiration. ​ Plants and their shade also create microclimates. Animal Kingdom ​ Coral reefs are home to more than 25 % of Earth’s marine species. ​ Tiny creatures called polyps create the coral reef. ▪​ The polyps have a symbiotic relationship with photosynthetic protists, such as dinoflagellates. ▪​ Therefore, reefs are only found in shallow, sunlit water. ​ Human activities such as mining, agriculture, pollution, and overfishing can threaten or destroy shallow-water habitats. ▪​ Stressed polyps reject the symbiotic protists, resulting in bleached, unhealthy reefs. ▪​ Protists cannot live in lower pH, acidic waters caused ​ by excess CO2. ​ Animals are divided into about 35 major phyla. ​ 6 Characteristics of animals include: ​ They are eukaryotic (having complex cells with membrane-bound organelles). ​ They have cells that lack cell walls. ​ They are multicellular. ​ They are heterotrophs that ingest food. ​ They are motile at some point in their life cycle. ​ They develop from a blastula early in their life cycle. ​ Both plants and animals show evolutionary change that reflects a movement of ancient species from water onto the land.  ​ Each major change is called an evolutionary milestone. ​ Many evolutionary milestones are marked by changes in body plan. 1.​ Body Plan: Each species has a unique body structure, called a body plan. ​ A body plan includes type of symmetry, presence of a body cavity, embryological development, segmentation, presence of a head, placement and number of limbs, movement, and the presence of a backbone. 2.​ Levels of Organization: While all animals have cells, how the cells are organized differs between species. ​ Cells are organized into specialized tissues, tissues can join together to form organs, and complex organ systems can form in some species. 3.​ Body Symmetry: This can reveal the evolution, movement, and interactions with other species. ​ Asymmetrical - no symmetry (corals) ​ Radial symmetry - shaped like a bowl or cylinder, with body pieces arranged around the centre like pieces of pie ​ Any longitudinal slice = two identical parts ​ There is no head or tail structures. Bilateral symmetry: mirror images on left and right sides, but top/bottom and front/back are different ​ Has anterior and posterior ends, dorsal and ventral surfaces on the top and bottom, and two similar lateral surfaces ​ This body symmetry works best for movement. ​ Allows for cephalization (development of a head) 4.​ Embryological Development: All animals begin as a zygote, which forms when a sperm fertilizes an egg. ​ The sperm and egg are haploid sex cells, containing half of the genetic information of a normal body cell. ​ The zygote is the first diploid cell of the new animal. ​ The zygote splits into two, then four, then eight, etc. ​ Eventually, a blastula (hollow ball of cells) forms, and begins infolding, resulting in the digestive tract and eventually all other organs and organ systems. ​ The blastopore is the first opening in the digestive tract. ​ Protostome = blastospore is a mouth ​ Deuterostome = blastospore is an anus ​ This is a developmental factor used to determine how closely related species are. 5.​ Segmentation (repeating parts): Many animals with bilateral symmetry are segmented into several repeating parts. ​ Annelids (earthworms) consist of a distinct head, tail, and several identical segmented rings. ​ Insects are segmented into a head, thorax, and abdomen. ​ The human backbone (right) shows segmentation. 6.​ Limbs (legs, flippers and wings): Animals with bilateral symmetry frequently have paired limbs. ​ Limbs can be used for movement, feeding, or gathering sensory information. ​ Animal phyla are often defined by appendages; antenna, mouthparts, wings, gills, legs, fins, arms, and tail parts. The phylogenetic tree of animals is difficult to define by time, as specific mileposts are hard to find. ​ Diversification occurred over a relatively short period of time, and there were many unique species that are now extinct. ​ Instead, the animal phylogenetic tree and its branches are defined by the similarities and differences in comparative anatomy, embryology, genetics, and molecular studies of living species. Initial branching is based on ​ the presence of tissues; ​ then by radial symmetry vs. bilateral symmetry; ​ then into protostomes or deuterostomes Like all evolutionary biology, this tree is likely to change based on future discoveries. ​ Notice the relationship between the phylogenetic tree and the branches and nodes. 1.​ Body plans 2.​ Level of organization 3.​ Body symmetry 4.​ Embryological development 5.​ Segmentation 6.​ Limbs ​ Vertebrates have a backbone; invertebrates do not. More than 98% of all animals are invertebrates. Invertebrates are NOT a branch on the phylogenetic tree because the lack of a feature cannot define a group. Many of the more complex animals, and those with which we are most familiar, are vertebrates. ​ Vertebrates make up most of the phylum Chordata.  ​ Vertebrates have a skull and a backbone, unlike all other animals. ▪​ The skull and backbone protect the central nervous system, including the brain. ​ Most vertebrates have structural support for paired limbs. ​ The phylogenetic tree of vertebrates uses a variety of evidence. ​ This phylogenetic tree is based on anatomical, molecular, and fossil evidence. Branches include: 1: presence of backbone 2: presence of hinged jaws 3: lungs or lung-like structures 4: having four feet (= tetrapod) 5: having an amniotic egg ​ (= waterproof) 6: producing milk for young 7: having feathers to conserve heat Human Impacts on biodiversity ​ Most human development occurs on or near the shores of large bodies of water or flowing rivers. ​ More than half of North America’s population lives along the Atlantic and Pacific coasts. ▪​ In addition, many people live near the Great Lakes or major rivers. ▪​ Coastal areas are also locations of substantial biological diversity. ▪​ Human activities can decrease biodiversity. ​ Dead zones occur when runoff from agriculture or sewage causes algal blooms in nearby water. ​ Building roads, dwellings, and factories pollutes the surrounding areas, and uses land and water. ​ Extinctions occur when a species completely disappears from Earth. ​ Mass extinctions occur when large percentages of all species become extinct (like the Cretaceous mass extinction that wiped out almost all dinosaur species). ▪​ These are usually caused by disasters like volcanic eruptions or asteroid impacts that change Earth’s climate. ​ We are in the midst of another mass extinction.  ▪​ 12 percent of the world’s bird species are endangered. ▪​ 300 species of plants (including 86 percent of moss species) in North America are at risk. ▪​ Many fish species are also threatened. 1.​ Habitat loss is the biggest threat to biodiversity. ​ IUCN estimates 50 percent of all threatened species are due to habitat loss. ​ Human development reduces available habitat. ​ Habitat fragmentation occurs when larger areas are split. ​ Large populations, expanding urban areas, large agricultural tracts, highways and rail links, the exploitation of natural resources, and even human indifference have all contributed to the loss of habitats. 2.​ Invasive species are the second-greatest threat to biodiversity. ​ Invasive species are non-native species that are harmful once they establish themselves in their new habitat. ​ They prey on native species, or outcompete them for resources. ​ They can be introduced accidentally or on purpose. ​ Kudzu was planted to control erosion. ​ The emerald ash borer arrived here in wooden crates carrying other materials. ​ Zebra mussels arrive in the ballast tanks of ships. ○​ There are now so many mussels in the Great Lakes they reduce O2 levels in the water. 3.​ Many human activities pollute the air, land, and water. ​ Burning fossil fuels, including coal for electricity, contributes large amounts of air pollution and CO2. ​ Acid rain forms when sulphur and nitrogen compounds are released from burning fossil fuels. ​ Many industrial processes use water for cleaning, cooling, or purifying, releasing polluted water back into ecosystems. ​ Pesticides are used to reduce the impact of destructive insects, fungi, and plants, but also pollute ecosystems. ​ Pesticides accumulate as they are passed up a food chain, harming each organism along the way. ​ Many Ontario communities have banned or restricted the use of pesticides. 4.​ Overexploitation occurs when humans harvest natural resources faster than the  resources can reproduce or be replenished. ​ The cod fisheries off Canada’s Atlantic Coast decreased from nearly 500 000 tonnes in 1988 to only 12 000 tonnes in 1996. ​ The cod population has not recovered, and many jobs in Atlantic Canada have been lost as a result. The rosy periwinkle, a cancer-fighting plant from Madagascar, was almost harvested to extinction before being planted commercially. 5.​ Many human activities result in the emission of CO2, methane, and other gases that cause global warming. ​ These activities include burning fossil fuels, slash-and-burn land clearing, burning peat bogs, raising livestock, and draining wetlands. 6.​ Global warming can lead to climate change. Effects of climate change include the outbreaks of disease, the forced migration of plants and animals, extreme weather events, more acidic environmental conditions, and decreased water quality and availability. ​ Synergistic effects are often greater than the sum of the impacts of these effects. Insects adapt to changing climate conditions quickly and will come into Disease Outbreaks increasing contact with humans. Since insects often carry disease, epidemics like SARS and H1N1 are more likely to occur. All plants have an optimal range of temperatures. As climate becomes more Plant Migration temperate in northern Ontario, grasslands will replace boreal forests. Animals have ideal climates where they are most successful. White-tailed deer and Virginia possum are now found hundreds of kilometres north of where they Animal Migration were 50 years ago. As animals migrate to new habitats, they change the natural balance of both their old and new ecosystems. Climate change has increased the number of extreme weather events throughout Canada, including major ice storms, droughts, and floods. Extreme Extreme Weather weather events can change the composition of an ecosystem and dramatically reduce levels of biodiversity in a short period of time — literally overnight. As increased CO2 levels dissolve in water, they can change the pH of the Increased CO2 water. Since aquatic organisms require a specific range of pH to survive, Levels they may die off. Water Availability Climate patterns will reduce the availability and quality of water in many and Quality arid (dry) and semi-arid regions. ​ Conservation biology attempts to lessen or eliminate the effects of biodiversity  loss. ​ Treaties and agreements are necessary, because plants, animals, and the weather do not know political boundaries. ▪​ The Convention on Biological Diversity is an agreement signed by 161 countries (including Canada) to strive to sustain biodiversity on Earth. ​ Ex-situ conservation attempts to protect species by removing them from their environment (eg.zoos, seed banks). ​ In-situ conservation attempts to protect species while they still exist in their natural habitats (eg.national parks, protected areas). ​ Ex-situ conservation is used when a species’ habitat is lost or threatened, or when the species’ numbers are very small. ​ Animals are kept in zoos, botanical gardens, or natural reserves. ​ Plants, their seeds, and their genetic information are kept in seed and gene banks. ​ Zoos (including the Metro Toronto Zoo) participate in Species Survival Plans (SSPs). ▪​ Breeding is done to increase genetic diversity. ▪​ Animals like the black-footed ferret may be re-introduced to their habitats if breeding programs are successful. ​ In-situ conservation is preferred to ex-situ. ​ Protected areas, habitat conservation, and laws to protect the threatened species and their habitat are used. ​ Conservationists are trying to re-introduce the Atlantic salmon to the Lake Ontario waterways by protecting its habitat. ​ The Karner blue butterfly became extirpated (locally extinct) in Ontario because of forest fire prevention. ▪​ When shade-intolerant species of grasses are allowed to grow in open spaces, the butterfly can successfully reproduce. ​ Many people, companies, and governments are trying to establish environmentally sustainable practices. ○​ Costa Rica fines heavy polluters and markets the country as an eco-tourism destination. ○​ Each of us can minimize our ecological footprint on the biosphere. ○​ Resources can be harvested, but at a rate that allows them to restore themselves naturally. ○​ These resources will therefore be available in the future, and can remain part of their ecosystems. ▪​ This improves biodiversity and ecosystem health. ○​ The challenge is to meet the needs of Earth’s human population while conserving ecosystems and resources to meet the planet’s other populations as well.