Unit I - Biodiversity 

## Ch 1.1 -Biodiversity - an introduction ### What is a species \ > **Biodiversity: the number of variety of species and ecosystems on Earth** > > **Species: all organisms capable of breeding freely with each other under natural conditions** > > **Morphology: the physical appearance and characteristics of an organism, the science of the study of these physical characteristics** > > \ > **Evolutionary change: a change that occurs in an entire population, usually occurs over a long period** \ A species is defined as a group whose members can freely breed among themselves under natural conditions → biological species concept \ Species are defined based on a set of physical characteristics/morphology when the traditional species definition does not apply \ Physical and behavioral changes that occur in the entire population of a species are referred to as evolutionary change --- ### Biodiversity \ > **Genetic diversity: the genetic variability among organisms, usually referring to the individual of the same species** \ Different species vary in behaviors, habitats, ecological niches and abundance, and genetic makeup as well --- ### Diversity in Ecology ✨ **Heterotroph: an organism that obtains energy by consuming living/dead organisms** Diversity is influenced by the total number of individuals present in an ecosystem → ecosystem with many large populations is considered more diverse The range of physical sizes, shapes, and distribution of the individual, as well as habitats and communities in an ecosystem is referred to as structural diversity → greater structural diversity can support a greater diversity of species as it has a great biodiversity **Food supply - between species and their food** * eg.1 - boneworms feed exclusively on bones of dead whales * eg.2 - the photosynthetic micro-organism performs photosynthesis and supplies the coral animals and clams with a steady supply of food **Protection - for shelter and protection** * eg.1 - hermit crabs use the shells of dead snails for a protective home * eg.2 - Cecropia trees provide shelter for a certain species of ants, and the ants protect the tree by biting and stinging herbivores **Transportation - move from place to place with the help of another species** * some flower mites climb onto the bills of hummingbirds moving from flower to flower * many seed have hooks that allow them to stick to passing animals → carried long distances before they fall off and begin growing **Reproduction - depends on other species for their own successful reproduction** * trilliums produce seed with fleshy tissues that attack ants and dispersed on them * many bird species build their nests in the abandoned tree cavities made by woodpeckers on their own nests **Hygiene - help maintain the health of another species** * coral reefs have “cleaning stations” where large fish come to have external parasites removed by small fish and shrimp * the bacteria that lives on our skin protect us from other bacterial and fungal infections **Digestion - living within digestive tracts are essential for food digestion** * a variety of bacteria and other micro-organisms lives within the termites’ guts to digest the wood * bacteria living in the large intestines of humans produce vitamins that are absorbed into the circulatory system --- ### Biodiversity at risk loss of biodiversity affects humans: * threatens food supply when entire species and plant varieties are lost * eliminates sources of natural medicines and potential new medicines * has a significant economic impact on tourism and forestry when accompanied by habitat destruction * has the potential to cause serious disruptions in biogeochemical cycles such as the carbon cycle A change in climate may make conditions too hot/cold, too wet/dry for species adapted to the original climatic conditions Human actions result in a rapid loss of natural habitats due to agriculture, forestry, urban expansion, the introduction of invasive species, over-harvesting of wild populations and serious water and air pollution * production of greenhouse gases → human-caused climate change --- ## Ch 1.2 - The Nature of Classification ### Taxonomy - Developing a Classification System Observing the morphology, behavior and even geographic location can be used to identify organisms → similarity in form, or evolutionary change challenges this way of identification --- ### Early Biological Classification Systems **Carl Linnaeus** Before Carl Linnaeus, it was common for species to be given one/more long descriptive names → Carl Linnaeus assign a binomial short name using binomial nomenclature **Traditional Taxonomic Levels** --- ### Dichotomous Key A dichotomous key is a structure in which a large set of items is broken down into smaller subsets → leading to the smallest available classification unit * provides an easy method of identifying a species --- ## Ch 1.3 - Phylogeny and Modern Taxonomy The theory of evolution states that all living things are descended from a common ancestor Taxonomy - the classification, identification, and naming of organisms - aims to group organisms according to how closely related they are to each other --- ### Phylogeny Phylogeny is the science that deals with evolutionary relationships between and among species → tracks relationships between entire species presented in a phylogenetic tree A clade is a taxonomic group that includes a single ancestor species and all its descendants * the tips of a branch on a phylogenetic tree can represent a particular species/an entire group of species --- ### Taxonomy Today Phylogenetic analysis can uncover the evolutionary relatedness of organisms → group into different-sized clades --- --- ## Ch 1.4 - Kingdoms and Domains --- ### Kingdom of Life Kingdoms - Animals, Plants, and Fungi, Eubacteria, (eukaryotic) Protists\\ **Eubacteria** * prokaryotic, cell walls contain peptidoglycan + unique compounds, and vary in shape and size * can be photosynthetic, chemotrophic/heterotrophic, can reproduce asexually * eg - Escherichia coli, Salmonella, Nitrogen-fixing bacteria **Archaea** * prokaryotic, cell walls and cell membranes contain peptidoglycan and have a unique structure, most are extremely small * some are extremophiles, live in the digestive tracks of mammals and marine environments, and all can reproduce asexually * eg - extreme thermophiles, methanogens **Protista** * eukaryotic, cells have extreme diversity of cellular structure, some have chloroplasts and cell walls * may be heterotrophic/photosynthetic/both, have variable forms of movement, usually live in aquatic/other moist environment, reproduce sexually and asexually * eg - amoeba, kelps, algae **Fungi** * eukaryotic, the cell wall is composed of chitin, most are multicellular, no not have chloroplasts * all are heterotrophic, most are terrestrial, and reproduce asexually and sexually * eg - mushrooms, yeast, molds **Plants** * eukaryotic, all are multicellular, cell walls are composed of cellulose, and possess chloroplasts * autotrophic and photosynthetic, most are terrestrial, reproduce sexually and asexually * eg - mosses, ferns, conifers, flowering plants **Animals** * eukaryotic, all are multicellular, cells do not have cell walls or chloroplasts * all are heterotrophic, most reproduce sexually, live in terrestrial and aquatic environments * eg - elephants, sponges, corals, insects, snails, birds, humans  --- ### Domains of Life In 1996, Carl Woese revealed that all organisms could be classified into three domains with different genetic makeups * Domain Eubacteria → Kingdom Eubacteria * Domain Archaea → Kingdom Archaea * Domain Eukaryotes → Kingdom Protista, Animals, Plants, and Fungi --- ## Ch 2.1 - The Prokaryotes: Eubacteria and Archaea --- ### Why Prokaryotes Are Important Bacterial diseases: cholera, leprosy, typhoid fever, strep throat, salmonella, poisoning, and tuberculosis Many bacteria (and some archaea) are decomposers and others are producer * recycle nutrients and are vital to biogeochemical cycles * fix/convert atmospheric nitrogen into compounds → photosynthetic bacteria are the major producers * humans rely on bacteria in the large intestine to produce needed vitamins K and B12 → mutualism * essential to the production of cheese, yogurt, soy sauce, and chocolate * bacteria also produced antibiotics → destroy and inhibit the growth of other micro-organisms * modified to produce medically valuable compounds - insulin and human growth hormone --- ### Domain Eubacteria **Proteobacteria (Purple bacteria)** * some used a different form of photosynthesis * ancient forms of the bacteria were the likely ancestors of eukaryotic mitochondria * some are nitrogen fixing * responsible for the bubonic plague, gonorrhea, dysentery, and some ulcers **Green Bacteria** * use a form of photosynthesis that differs from other eukaryotes * usually found in salt-water environments/hot springs **Cyanobacteria (Blue-green algae)** * uses a form of photosynthesis similar to plants and other eukaryotes * ancient forms of these bacteria were the likely ancestors of eukaryotic chloroplasts * play a major role as producers and nitrogen fixers in aquatic ecosystems * form a symbiotic relationship with fungi **Gram-positive bacteria** * cause many diseases such as anthrax, strep throat, bacterial pneumonia, and meningitis * used in food products such as yogurt and probiotic products with lactobacillus * some lost their cell walls **Spirochetes** * their spiral-shaped flagellum is embedded in their cytoplasm * move with a corkscrew motion * cause syphilis * symbiotic spirochetes in termite intestines digest wood fiber **Chlamydias** * all are parasites that live within other cells * cause chlamydia, an STI * cause trachoma, the leading cause of blindness **Characteristics** * chromosome is a single loop of DNA (deoxyribonucleic acid) found in the nucleoid * ribosomes used in protein synthesis are scattered throughout the cytoplasm * have one/more flagella for movements and pili → pili are made of stiff proteins that help the cell attach to other cells/surface * have one/more plasmid in the cytoplasm → a small loop of DNA that carries a small number of genes → not essential to the function but give antibiotic resistance * have complex cell walls composed primarily of peptidoglycan → the cell wall become strong and rigid when the chains cross-linked * some have a sticky capsule → reduce water loss, resists high temperatures and helps keep out antibiotics and viruses ### **Metabolism** Autotrophic bacteria make their own food → assemble complex C molecules from simple inorganic chemicals (eg. H2O, CO2, and minerals) Heterotrophic bacteria get their nutrients from C containing organic chemicals found in other living organisms/their remains The primary sources of energy for living things are sunlight and chemical * organic molecule - sugar, fats, proteins * inorganic molecule - H2, sulfur, and iron compounds Obligated aerobes - animals and plants → need oxygen obtained by respiration to get energy from food Facultative aerobes → perform aerobic respiration in the presence of oxygen and anaerobic respiration/anaerobic fermentation when oxygen is absent Obligated anaerobes → can’t live in an environment where oxygen is present ### Reproduction **Binary Fission** * produce two daughter cells with identical genetic material (chromosomes and plasmids) * cell elongates and DNA is replicated → cell wall and plasma membrane begins to divide → cross-wall forms completely around divided DNA → cell elongates * copying begin error result in mutation/changes in the genetic makeup → increase the genetic diversity **Conjugation** * a bacterial cell passes a copy of a plasmid to the nearby cell through a hollow pillus → may benefit the nearby cell * considered sexual reproduction **Horizontal gene transfer** * transformation occurs when a cell picks up a loose fragment of DNA from its surroundings and uses it → DNA fragment came from a different species Some bacteria produce a highly resistant structure that forms around the chromosome called an endospore * withstand extreme conditions and remain dormant until conditions improve ### Bacterial Diseases some infectious bacteria can cause diseases by producing and releasing toxins * botulism food poisoning - toxin released by ***Clostridium botulinum*** → cause muscle paralysis * severe food poisoning - the releasing of toxin after ***E. coli*** cells die → water contamination (a case of horizontal gene transfer) ### Antibiotics and Antibiotic Resistance Antibiotic substances are produced by prokaryotes and fungi as a form of chemical warfare Overuse of antibiotics can cause bacteria to adapt and become resistant * resistant bacteria is most likely to survive and reproduce when exposed to antibiotics → resistant bacteria make up more of the population → bacteria become more resistant and make the antibiotics ineffective ### Gram Stain most bacterial cell walls contain peptidoglycan * a polymer composed of modified sugars cross-linked by short polypeptides * archaeal cell walls contain polysaccharides and proteins but no peptidoglycan → Gram Stain test can classify bacterial species as Gram-positive and Gram-negative | Gram + | Gram - | |----|----| | positive result in the test | negative result in the test | | take up crystal violet stain | alcohol degrades cell wall allowing crystal violet stain to wash away | | look purple under the microscope | take up the counter stain and appear pink | | have thick peptidoglycan layer that retains the stain | thin peptidoglycan layer | | more receptive to antibiotics | less receptive due to outer membrane | --- ### Domain Archaea * have unique chemical makeup in their cell membranes and walls and lack peptidoglycan * many inhibits extreme environments as the cell membranes and cell walls are more resistant to physical and chemical disruption **Methanogens** * live in low-oxygen environment such as sediments of swamps and lakes, digestive tracks * generate energy by converting chemical compounds into methane gas which is released into the atmosphere **Halophiles** * salt-loving organisms that can live in highly saline environment such as the Dead Sea * most are aerobic and get organic food molecules * some uses light as a secondary energy source **Extreme thermophiles** * live in extremely hot environments including hot springs and hydrothermal vents * optimal temperature range for growth is 70 - 95C **Psychrophiles** * cold-loving organisms found mostly in the Antarctic and Artic oceans * optimal temperature range for growth is -10 to -20C --- ## Ch 2.2 - Viruses, Viroids, and Prions ### Viruses * small, non-living particles * consists of genetic materials surrounded by a capsid made of protein * do not have cytoplasm * can’t grow/reproduce on their own * don’t produce/use energy * don’t create waste * contain DNA/RNA that carry information that provides instructions for synthesizing protein molecules * infectious and are passed from cell to cell → control the cell of the host cell ### Why viruses are important Viral diseases include * mild symptoms: common cold, chicken pox * serious/deadly symptoms: AIDs, cholera, rabies * easy transmission: influenza virus DNA virus * hepadnavirus → hepatitis B * herpesvirus → cold sores, genital herpes, chicken pox * adenovirus → respiratory infections, tumors RNA virus * paramyxovirus → measles, mumps, pneumonia, polio, common cold * retrovirus → HIV/AIDS * rhabdovirus → rabies ### Classification and Phylogeny * classified into orders, families, genera, and species * most can infect only one singular host species/closely related host → might infect only one organ system/single tissue/cell type * eg.1 Human Immunodeficiency Virus (HIV) - only infect certain immune system cells * some can infect many species → rabies can infect all mammals and birds * bacteriophage → inject DNA into the bacterium while the protein capsule remains outside ### Origin and Characteristics of Viruses * originated as small infectious cells and lost their cytoplasm and ability to reproduce outside a living cell over time * suspected that viruses originated as “escaped” fragments of DNA/RNA molecules * \ all consist of an RNA/DNA molecule surrounded by a capsid, and some are surrounded by an envelope→ envelop is created when a virus leaves a host cell and part of the host cell membrane wraps around the virus  ### Infectious Cycle **Lytic Cycle** 1. the virus binds to the surface of the host cell and inserts its DNA into the cell’s cytoplasm 2. the viral DNA forms a loop and may enter the lysogenic/lytic cycle 3. the viral DNA constructs the cell to make and assemble new viral DNA and capsids 4. lysis occurs as the host cell bursts **Lysogenic Cycle** 1. the virus binds to the surface of the host cell and inserts its DNA into the cell’s cytoplasm 2. the viral DNA forms a loop and may enter the lysogenic/lytic cycle 3. the viral DNA gets inserted into the bacterial chromosomes 4. the viral DNA has replicated along with the bacterial DNA every time the cell divides 5. the viral DNA separates from the bacterial chromosome when activated 6. the viral DNA constructs the cell to make and assemble new viral DNA and capsids 7. lysis occurs as the host cell bursts  ### Vaccination and Human Health Vaccines are mixtures that contain weakened forms/part of a virus → trigger a response by the immune system without causing infection after injecting into the body → creates a chemical “memory” that allows the immune system to react quickly if the individual comes in contact with the real virus → reduce human suffering and save lives → some diseases like AIDS is not suitable for developing effective vaccines → structure and characteristics of the infection/constant changes that makes it ineffective the next year ### Putting viruses to work * using a virus capsule to deliver a drug → used to deliver drugs to targeted cells in the body - eg. deliver chemotherapy drugs to cancer cells * using a virus to insert a new copy of a gene → used to insert corrective genes into individuals who suffer from genetic disorders * using a virus to insert a gene taken from one species into another species → used to create genetically modified organisms, used in GMO crops --- ### Viroids and Prion **Viroids** * small, infectious pieces of RNA * smaller than viruses and do not have a capsid * RNA does not code for protein * plant pathogens * may interfere with the normal formation and functioning of RNA within the host cell **Prions** * proteinaceous infectious particles * found in the brain and nervous tissues of an infected animal * enter the bloodstream and go to the brain → interact with normally shaped protein → cause those proteins to change the shape and become abnormal and infectious → brain full of spongy holes --- ## Ch 2.3 - Protists Most are aquatic but are terrestrial --- ### Why Protists are Important Protists perform photosynthesis along with some prokaryotes → major producers in the world’s ocean * non-photosynthetic protists are important consumers Many protists are parasites → do not harm host organisms, but can cause serious diseases * eg.1 - **Plasmodium** (single-celled protist) - causes malaria * eg.2 - sleeping sickness and amoebic dysentery * eg.3 - **Giardia lamblia** (intestinal parasite of humans) - causes giardiasis → causes abdominal pain, diarrhea, and chronic inflammation of the gut --- ### The Origins of Eukaryotes protists were the first eukaryotes → have nucleus and organelles bound by membranes * developed from the folded cell membrane of ancestral prokaryotes → increase cell surface area allowing a better exchange of materials Mitochondria and chloroplasts are thought to have originated from endosymbiosis → once a prokaryotic organism that was engulfed by an early anaerobic eukaryotic cell * each has two membranes * inner membranes are similar to those of the ancestral prokaryote, and outer membranes match the cell membranes of eukaryotes * have their internal chromosomes similar to prokaryote chromosomes and contain genetic information used by the organelles * reproduce independently within eukaryotic cells by binary fission → mitochondria were believed to be aerobic prokaryotes relating to modern proteobacteria → chloroplasts were believed to be photosynthetic prokaryotes relating to modern cyanobacteria ---  --- ### Characteristics * eg.1 - Heterotrophic paramecia * macronuclei → control the metabolism and are responsible for the normal functioning of cells * micronuclei → responsible for controlling reproduction, genetic reorganization during conjugation, and production of macronuclei * contractile vacuoles → contract to eliminate excess water * gullet → taking in food * cilia → moving * trichocysis → release long fibers for defense ***Euglenoids -*** photosynthetic autotrophs * unicellular * two flagella for moving * outer surface covering consist of stiff proteins ***Cilliates*** - heterotrophs * unicellular * complex internal structures * have cillia for movement but no cell walls **Apicomplexa -** heterotrophs * unicellular * no cell wall * parasites **Diatoms -** photosynthetic autotrophs * unicellular * move by gliding * covered by glass-like silica shells ***Amoebas -*** heterotrophs * have hard outer skeletons * move by extensions of the cytoplasm called pseudopods **Slime Molds -** heterotrophic decomposers * have unicellular and multicellular stages * move with flagella/pseudopods **Red algae -** photosynthetic * almost all are multicellular * no cilia/flagella * cell walls are made of cellulose --- ### Interactions in Ecosystems Protists play key roles are producers/consumers * eg.1 - green, red, and brown algae (seaweeds) - gas-filled bladder help produce energy through photosynthesis → primary producers in aquatic food webs Climate change is affecting many protists * eg.1 - the rising temperature in oceans and lakes, and water is becoming acidic → affect protists’ ability to produce outer protective shells and the increase in some species → may not survive → may damage the food chain * eg.2 - the **zooxanthellae** lose their green chlorophyll pigment when the corals are stressed by pollution/warm temperature → coral appears bleach white → die --- ### Life Cycle Single-celled protists reproduce asexually and sexually * asexual: binary fission - cell divides into two genetically identical daughter cells → macronucleus elongates and divides → all organelles are divided equally between the daughter cells * sexual: conjugation - cells align and exchange genetic materials (some involve the exchange of special micronuclei) * sexual: formation of zygote - the haploid sex cells fuses together 1. Diploid sporophytes produce and release single-celled haploid spores 2. find and attach to a surface and begin dividing and growing into multicellular haploid gametophytes 3. produce haploid sperm and eggs 4. becomes a diploid zygote and grows into a multicellular sporophyte → asexual and sexual reproduction are needed to complete a full cycle of alternation of generation * eg.1 - **hydra** - can reproduce through sexual reproduction or diploid reproduction with buds that resemble the original adult 1. ***Plasmodium*** zygote pass through the gut wall and develop into oocysts that produce many haploid sporozoites by meiosis 2. injected into the blood which will be carried to the liver 3. sporozoites reproduce asexually in liver cells containing merozoites 4. merozoites enter the blood stream and invade red blood cells, reproducing asexually → ROC die and release merozoites → cause chills and fever 5. some merozoites in RBC develop into immature male and female gamete cells which are released into the bloodstream 6. female mosquito ingest blood from an infected human and the gamete matures in the mosquito’s gut, and then fuse to form zygote --- ## Ch 3.2 - Plants \ > **Biodiversity: the number and variety of species and ecosystems on Earth** \ ### What is a Species? \ > **Species: all organisms capable of breeding freely with each other under natural conditions** > > \ > **Hybridization: the cross-breeding of two different species** > > \ > **Morphology: the physical appearance and characteristics of an organism, the science of the study of these physical characteristics** \ A species is a group whose members can freely breed among themselves under natural conditions → biological species concept \ Species are defined based on a set of physical characteristics/morphology --- ### Variation over Time and Space \ > **Evolutionary change: a change that occurs in an entire population, usually occurs over a long period** --- ### Biodiversity \ > **Genetic diversity: the genetic variability among organisms, usually referring to individuals of the same species** \ Species vary in their behavior, habitats, ecological niches, and abundance * genetically diverse --- ### Diversity in Ecosystem \ > **Heterotroph: an organism that obtains nutrients by consuming living / dead organisms** > > \ > **Autotroph: an organism that uses sources of energy to produce nutrients from the water, gases, and/or minerals** > > \ > **Species diversity: a measure of diversity that takes into account the quantity of each species present, as well as the variety of different species present** > > \ > **Structural diversity: the range of physical shapes and sizes within a habitat/ecosystem** \ **Diversity of Interactions** \ The important activities and processes of one species may depend entirely on another species for success → contribute to the stability and productivity of their ecosystem \ Diversity is influenced by the total number of individuals present in an ecosystem → ecosystem with many large populations is considered more diverse \ **Diversity of Habitats** \ The range of physical sizes, shapes, and distribution of individuals, as well as habitats and communities in an ecosystem → structural disversity \