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Summative Grade 11 AP Biology Prokaryotes

Prokaryotes are extremely common Can be found almost everywhere (bacteria) o Soil o Air o On organisms/in them o Every possible place that has favourable living conditions Archaea can also be found in extreme conditions Their collective mass is at least 10 times that of all eukaryotes Bacterial Cell Wall Formed by peptidoglycan Stain either Gram-positive or Gram-negative (see classifying bacteria) Peptidoglycan encloses the entire bacterium and anchors other molecules that extend from its surface. Difference from plant cell wall: plant cell walls are formed mainly by cellulose Classifying Bacteria Gram stain, developed in the 19th century Gram-positive bacteria have similar walls with a relatively large amount of peptidoglycan (thick protein layer on their cell wall and stains purple) Gram-negative bacteria have less peptidoglycan and are structurally more complex, with an outer membrane that contains lippolysaccharides. (carbohydrates bonded to lipids.) (thin protein layer on their cell walls and stain pink) Classified by shape, structure of their cell walls, and their source of food and energy Bacterial phylogenies have been constructed based on analysis of RNA sequences Genetic change by mutation occurs rapidly in bacteria Genetic differences can arise in bacteria populations within a few generations Bacterial Locomotion Flagella- may be scattered over the entire cell surface or concentrated at one or both ends of the cell Taxis- movement toward or away from a stimulus, chemotaxis- respond to chemicals by changing their movement patter Ex: movement toward nutrients/oxygen (positive chemotaxis), away from toxic substances (negative chemotaxis) Bacterial Reproduction (asexual) Binary Fission

Bacteria makes copy of its single chromosome, and when cell reaches a certain size, it elongates and separates the two chromosomes (chromosomes attached to cell wall by cytoskeleton). The cell then builds parition between them and the septum forms Septum is completed and distinct cell walls form

Genetic Modifications of Bacteria Conjugation Two bacteria cells are linked to each other through pilus (bridging structures) One bacterium transfers all or part of its chromosome to another across the pilus Receiving cell undergoes binary fission to produce more cells with the new gene content Transformation The modification of genotype of a cell by the introduction of DNA from another source Ex: plasmid (small loops of DNA separate from the main chromosome), contains one to few genes, these genes are different from those found in the chromosomes, can split from the bacterial chromosome and rejoin it, important in producing genetic recombination in bacteria Transduction Transfer of genetic material by phages (viruses) as they infect one cell to another Nutritional Categories of Bacteria Photoautotrophs Use light as their source of the needed energy and CO2 to form organic compounds Photoheterotrophs An organism that depends on light for most of its energy and principally on organic compounds for its carbon Chemoautotrophs Use CO2 and oxidize inorganic substances to obtain energy Chemoheterotrophs Oxidation/consummation of organic molecules to generate energy and to obtain carbon Classification of Prokaryotes into two Domains Carl Richard Woese defined Archaea in 1977 by phylogenic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese. Molecular systematics is the use of the structure of molecules to gain information on an organisms evolutionary relationships. The study of rRNA molecule led him to conclude that Archaeans are more closely related to Eukaryotes than bacteria, thus forming their own group. Ecological Significance of Prokaryotes Bacteria: decompose detritus and turn organic carbon into inorganic carbon Nitrogen fixing bacteria (nutrients for plants) and denitrifying bacteria Symbiotic relationships with eukaryotes

Key characteristics of the three domains Domain Bacteria Characteristics Cocci, bacilli, and spirals Most unicellular, some species form colonies Membrane-bound organelles absent Peptidolycan in cell walls Circular chromosome Nucleoid RNA polymerase: 1 Rare introns Antibiotics inhibit growth (streptomycin and chloramphenicol Histones associated with DNA absent Initiator amino acid for protein synthesis: Formyl-methionine Membrane lipids- unbranched hydrocarbons Membrane-bound organelles absent Nuclear envelope absent Peptidoglycan in cell wall absent Membrane lipids : some branched hydrocarbons Several kinds of RNA polymerase Introns present in some genes Antibiotics dont inhibit growth (streptomycin and chloramphenicol Histones associated with DNA present Circular chromosomes Initiator amino acid for protein synthesis: Methionine Nuclear envelope present Membrane-bound organelles Peptidoglycan in cell wall absent Membrane lipids: unbranched hydrocarbons RNA polymerase: several kinds Initiator amino acid for protein synthesis: Methionine Introns present Response to the antibiotics streptomycin and chloramphenicol: Growth not inhibited Histones associated with DNA present

Archaea

Eukarya

Eukaryotes
Protists Diversity Most protests are unicellular, although there are some colonial and multicellular species. At the cellular level, many protists are the most nutritionally diverse of all eukaryotes. There are autotrophs, heterotrohps, and mixotrophs. There habitats are also very diverse.

Most protists are aquatic, and are found almost anywhere with water. They are important constituents of planktons. Reproduction and life cycles are highly varied. All three basic types of sexual life cycles are represented among protists, along with some variations that do not quite fit any of types. Asexual reproduction. Too many structural and functional differences among them. Genesis of eukaryotes from prokaryotes Endosymbiosis- origins of mitochondria and plastids(chloroplasts) - according to this theory, these organelles originated as separate prokaryotic organisms that were taken inside the cell as endosymbionts. Kindom Protista Characteristics Heterotrophs and autotrophs Most are single celled Eukaryotes Do not fit in other kingdoms Less diverse than bacteria, more diverse than other eukaryotic kingdoms Heterotrophs- feed by releasing digesting enzymes into their surroundings, absorb the digested nutrients into their cells Few are unicellular Boundary of a fungal cell is a cell wall made of chitin instead of cellulose Hyphae+septa Sexual+asexual reproduction Vascular + non-vascular Autotrophs Roots, stems, leaves Alternations of generations Cellulose cell walls Have chlorophylls a and b Photosynthesis Aquatic or terrestrial Gymnosperms or angiosperms Multicellular Eukaryotes Mostly sexual reproducation Multicellular Eukaryotes Reproduce sexually Ingest food Aerobic Heterotrohps Herbivore, omnivore, carnivore

Fungi

Plants

Animalia

Kingdom Fungi
Acquiring Nutrients Hyphae grows across a source of food (dead matter) Release digestive enzymes Enzymes break down large organic molecules in the substrate into smaller molecules Smaller molecules diffuse into the fungus for growth and repair (extracellular digestion) More extensive the mycelium, greater surface area available for absorbing nutrients Some are parasites of plant and animals that specialized to feed on living cells, their hyphae is called haustoria that penetrate host cells Hyphae is a network of fine filaments. Mycelium is a loose, branching network of hyphae (Hyphae strung together form a network called mycelium) Fungal Cell Walls Chitin, a protein that makes up the cell wall of fungus cells Contributions to an Ecosystem Decomposers: break down organic waste and release nutrients into the soil Performing essential recycling of elements between the living and nonliving world They form symbiotic relationships with plants, algae, and animals. We eat fungi. Use others to make cheeses, alcoholic beverages and bread Antibiotics produced by fungi treat bacterial infections Fungi is leading to applications in biotechnology Phyla of Fungi Phylum Zygomycetes Basidiomycota Ascomycota Chytridiomycota Blastocladiomycota Neocallimastigomycota Glomeromycota Characteristics Saprotrophs, few parasites of protests and small invertebrate animals, mostly terrestrial, ex: Rhizopus stolonifer (black bread mold), Pilobolus (grows on animal dung) Have short lived reproductive structure ex: mushrooms, rusts, smuts, shelf fungi/bracket fungi Largest group of fungi, have asci, mostly saprotrophs, parasites of plants, sexual reproduction ex: truffle, Aspergillus nidulans Water mould -Allomyces sap, Batrachochytrium dendrobatiolis

Kingdom Animalia
Hypothesis for the origins of Animals Most systematics now agree that all animals lineages are monophyletic; that is, we can trace all lineages back to a single common ancestor. The ancestor was probably a flagellated protist; which was probably related to choanoflagellates. Two forms of symmetry of the Eumetazoa (clade comprising all major animal groups except sponges, placozoa and several other little known animals) Bilateral : has a left and a right side, one line of division that allow the body to be divided into equal but opposite parts Radial: parts of animal radiate from the centre. Any imaginary slice through the central axis divides the animal into mirror images Cephalization as an Evolutionary Trend The nervous tissue, over many generations, becomes concentrated toward one end of an organism. This process eventually produces a head region with sensory organs. The end of a traveling animal that is usually first to encounter food, danger, and other stimuli. development of central nervous system and adaptation for movement on land. Germ Layers of Radiata and other Eumetazoa Radiata contain two germ layers including the ectoderm and endoderm, the other Eumetazoa differ in that they have an additional layer called the mesoderm. Classifying Animals Term Acoelomates Significance Animals with no blood vascular system and lacking a cavity between the gut and outer body wall ex: flatworm -major split in phylogenic tree for animal development involved the split of bilateral organisms into two further branches Animals with fluid-filled body cavity that is not enclosed by mesoderm (body cavity formed from the blastocoel) ex: roundworms A coelom is a fluid-filled body cavity found between the body wall and gut that has a lining. It comes from the mesoderm. Branches from Coelomates, a bilateral animal whose first embryonic indentation eventually developes into a mouth (mouth develops from blastospore) ex: annelids, arthropoda, mollusks A branch from Coelomates that includes chordates and echinoderms. The first indentation of their embryos eventually develops into the anus (anus develops from blastospore)

Pseudocoelomates Coelomates Protostomes Deuterostomes

Blastospore: the indentation that during gastrulation leads to the formation of the archenteron

Major differences between Protostomes and Deuterostomes Protostomes: blastospore develops into mouth and the second opening forms the anus Early cell division: cells specialize, determined cleavage Coelom formation: schizocoelous-coelom originates as a split within a bud of mesodermal tissue at time of gastrulation Deuterostomes: blastospore develops into the anus and the second opening forms the mouth Early cell division: undetermined cleavage Coelom formation-enterocoelous: coelom originates from an out pocketing of the archenterons during gastrulation Phyla of Animalia Phylum Ponifera Cnidaria Platyhelminthes Annelida Mollusca Arthropoda Echinodermata Chordata Characteristics Sponges Polyp/medusa, ex: jellyfish Flatworms Segmented worms, long tube like bodies, each segment contain similar sets of organs for excretion, circulation, nerve control Soft-bodied animals Joint legged animals, body segments, hard external cuticle, legs divided into moveable segments, ex: spider Starfish Vertebrate/invertebrate

Sponges and their method of Nutrition Sponges filter their food from passing stream of water. The body has a single opening food enters, waste matter leaves A sponge is long and cylindrical with an opening in the middle. They have no tissue or organs. Unique characteristics of Cnidarians These organisms are of radical symmetry Lack a mesoderm Body is a digestive sac that can be one of two types Use tentacles to capture and eat prey Body plan is a sac like with a central digestive compartment, with gastrovascular cavity and it has a single opening The two shapes Polyp (asexual): cylinder-shaped and lives attached to some surface Medusa: flat and roams the waters looking for food

Platyhelminthes Evolutionary Significances Structurally more complex 3rd embryonic layer, mesoderm, contributes to the development of more complex organs and organ systems, including true muscle tissues Significance to Humans cause troublesome diseases in humans tapeworms reside in the enteron or the biliary ducts of mammals parasites on humans cause much suffering and sometimes death cause diseases in livestock which can cause problems for humans some parasite on neural system Parthenogenesis Biological reproduction that involves development of a female (rarely male) gamete without fertilization. It occurs commonly among lower plants and invertebrate animals, particularly rotifers, aphids, ants, wasps, and bees. An egg produced parthenogenetically may be either haploid or diploid. Unique Structure and Function of the Pseudocoelomates Mesoderm discontinues with regard to endoderm but not contact with ectoderm Provides anchor matrix of muscle fibres etc. derived from suspension of digestive system; fluid-filled cavity, therefore hydrostatic pressure provides support for overall body structure and shape of organism. Nematodes and Humans Are roundworms found in moist environments Trichinosis is caused by a roundworm that infects meat products (usually pork) Humans ingesting infected meat can become afflicted with this disease Parasites of humans Important role in decomposition and recycling nutrients Research specimens (aging in humans) Agricultural pests that attack roots of plants Body Regions of a Mollusk Muscular foot Visceral Mass Mantle Mollusks and Annelids The life cycle of many marine molluscs includes a ciliated larvae called the trochophore, also characteristics of marine annelids and other Protostomes. But mollusks lack the one trait that most defines annelid heritage: true segmentation.

Annelids Evolutionary significance Muscles work against the non-compressible coelic fluid, a hydrostatic skeleton Muscles can alter the shape of each segment individually because the coelom is divided into separate compartments. Segmentation Segmentation allows for a high degree of specialization of body regions. This regional specialization is an evolutionary development of the body plan of arthropods. Easier motility Parapodia (pair of them) (satae) that function in locomotion (in each segment of a polychaete) Arthropoda Success

Greater diversity in distribution and numbers than any other phyla of Animalia Have adapted successfully to life in water, on land, and in air Live on top of mountains, at great depths in the ocean and in Antarctica Can survive extremes of temperature, toxicity, acidity and salinity Characteristics for the Success Hard external cuticle, acts as an exoskeleton for muscle attachment Segmentation Jointed legs Coelomate Deuterostomes: echinoderm and chordata, mammals Unique Traits of Echinoderms Water vascular system- a network of hydraulic canals branching into extensions called tube feet (podia) that function in locomotion, feeding and gas exchange By expanding or contracting various chambers in the water vascular system, water is forced into the tube feet, extending or retracting them and allowing echinoderms to walk Majority benthic organisms (live on sea floor) Most show pentamerous radial symmetry Bilaterally symmetrical larvae Characteristics of Chordates Have a dorsal nerve cord, and from it, nerve braches to all parts of the body Have a notochord which is a rod of cartilage that runs along dorsal length of body In most vertebrates, notochord only occurs in embryo

Have gill slits in pharynx (throat), terrestrial vertebrates only have them in embryonic stage.

Example of an invertebrate chordate: a tunicate, hagfishes- they lack a series of backbones in their body -Urochordata Paedogenesis Reproduction by an animal that is still in the larval or pre-adult form. Paedogenesis is a form of neoteny and is particularly marked in the axolotl, a larvae form of salamander, which retains its larvae features owing to a thyroid deficiency but can breed, producing individuals like itself. If the thyroid hormone thyroxine is given, metamorphosis occurs. An example is the mudguppy, which retains gills and other larval features when sexually mature. Characteristics of Subphylum Vertebrata Series of bones that make up the back bone Craniates (having more complex nervous system) Significance of being a Tetrapod 4 feet limbs that can support their weight on land and feet with digits that allow them to transmit muscle generated forces to the ground when they walk live on land bones of the pelvic girdle, to which the hind legs are attached, are fused to the backbone, permitting forces generated by the hind legs against the ground to be transferred to the rest of the body. Amniotic Egg and the Amniote Amniotic egg contains specialized membranes that protect the embryo (humans --> amniotic sac). The shell around the egg slows dehydration. Amniotes also have skin thats less permeable and the ability to use the cage to ventilate the lungs. This allowed tetrapods to reproduce on land. Major Branches of Subphylum Vertebrata Class Characteristics Aves Endothermic, feathered over much of body surface; scales on legs and feet; bones hollow and light-weight in flying species; four chambered hear; well developed lungs and air sacs for efficient gas exchange Reptilia Have scales that create a water proof barrier, lay shelled eggs on land, ectothermic; most have three chambered hearts; internal fertilization; amniotic egg typically laid on land Mammalia Mammary glands which produce milk; hair; generally larger brain than other vertebrates of equal size; endothermic; subcutaneous fat; hair; most viviparous; suckle young with milk produced from mammary glands; four chambered heart; most have four legs; Amphibia Most have moist skin that complements the lungs in gas exchange

Osteichthyes

Agnatha Cephalochordata Chondrichthyes

Bony fishes; bony endoskeleton; aquatic; ectothermic; well developed respiratory system, usually involving gills; possesses swim bladder; paired fins; divided into two groups: ray finned fishes (which include most living species) and lobe finned fishes (which include the lungfish and coeloacanth) Jawless fishes-exclude all jaw fish (vertebrates) Lancelets- larvae filter feeders; adults parasites whose circular mouth is lined with rasping toothlike structures; many live in both salt water and fresh water during the course of their lives Cartilaginous fish: have jaws; most live in salt water; typically several gill slits; tough small scales with spines; ectothermic; two chambered heart; male possesses structures for internal fertilization

Kingdom Plantae
Characteristics of all Plants apical meristems alternation of generations walled spores produced sporangia multicellular gametangia multicellular dependent embryos Advantage of Living on Land more sunlight more access to CO2 more habitat more nutrients Tissue in Land Plants (most of them) The vascular tissue (includes the xylem and phloem transport materials to all parts of the plant xylem: water superhighway for the plant, transporting water throughout the plant the phloem: transports sugar and nutrients to the various plant structures Major groups of Plants Non-vascular plants- without vascular tissue (bryophytes: mosses) Vascular plants- with vascular tissue (angiosperms and gymnosperms) Reproductive Strategies Non-vascular plants require moist habitats because their sperms must swim through water to fertilize the ovule. Vascular plants can live in dry climate because they do not require water for fertilization. They can use wind and animals.

Ferns Water dependence Fern species live in a variety of habitats, from remote mountain elevations, to dry desert rocks faces, to bodies of water or in open fields. Some live in extremely acidic habitat and other live in basic ones. They are vascular plants and do not require a lot of water even though they lack seeds and flowers. Although their preferred habitat is a moist one, they can survive in dry areas as well. They do not entirely depend on water for reproduction. Major Groups that Reproduce Using Seeds Gymnosperms- naked seeds Angiosperms- flowers plants Significance of the Angiosperms Protect their seeds within the body of a fruit Seeds are better protected of nutrients Can be carried to farther places and can be displaced farther than those of gymnosperms Flowering plants Major Strategies for Plant pollination Seeds (gymnosperms + angiosperms) Anemophily (wind) Hydrophily (water) Biotic pollination : organisms that transport pollen Entomophily (insects) Zoophily (vertebrates, ex: birds and bats) Development of Fruit Various fruit adaptations help disperse seeds Dandelions: fruit function like propellers--> wind Coconuts: dispersal by water Burrs: cling to animal for dispersal Edible fruits: animal eats --> deposit seeds with feces--> acts like fertilizer It helped plants to be dispersed to a larger area and become more wide spread. Their seeds are also protected.

Virus
Living Things? Not considered living things Have no cellular structure

No cytoplasm, organelles or cell membranes Do not carry out respiration or any other common life processes Consist of little more than strands of RNA or DNA surrounded by a protective protein coat called a capsid Parasite cells; capsid protects the virus from attacks by the host cell enzymes.

Structure of Virus Tobacco mosaic virus : helical capsid with the overall shape of a rigid rod Adenoviruses: a polyhedral capsid with a glycoprotein spike at each vertex Influenza viruses: outer envelope studded with glycoprotein spikes. The genome consists of eight different RNA molecules, each wrapped in a helical capsid Bacteriophage T4: like T-Even phages, has a complex capsid consisting of a polyhedral head and a tail apparatus Depending on the virus, the capsid may be rod-shaped, polyhedral, or more complex shape Characteristics that led to a Classification of Viruses into 21 Groups

Life Cycle Lytic cycle 1. Attachment 2. Entry: the virus inject its nucleic acid into the host cell 3. Replication: hosts metabolism replicates the viral RNA or DNA 4. Assembly: new virus particles are assembled 5. Lysis and Released: host cell breaks open and release new viruses Life Cycle of Provirus Enzyme called reverse transcriptase causes the host cell to copy the viral RNA into DNA Viral genome can enter the chromosomes of the host cell and can be copied whent the cell divides Virus is now called a provirus When host cell undergoes mitosis, it replicates the provirus Process can continue for years and does not kill host cell However, provirus can separate from host chromosomes and complete the lytic cycle Why Viruses are Important for Humans

Biotechnology The gene is spliced into the genome of a virus The virus gets copied with the gene through host cell Helps genetic engineers Cancer Research Can possibly cure cancer Still under research People who had cancer and caught a severe virus and survived are cancer free Origin of Viruses Scientist believe that they evolved after the first cells They cannot replicate without host cells Probably originated as fragments of nucleic acid that escaped their original acid Survived by becoming parasites of same or similar types of cells

Taxanomy
Taxa Domain Kingdom Phylum Class Order Family Genus Species

Binomial Nomenclature Two-word name for each species Latinised and first word always describe the genus of the species First letter of the first word is always capitalized Second word is a particular name given to the species that no other species have within the same genus Common names are misleading; same name can be given to two completely different species With scientific naming, no two species have the same name Sources of Genetic Variety Mutation Meiosis (sexual reproduction)

Meiosis allows different gene combinations Crossover occurs where homologous chromosomes have the potential to exchange bits of DNA Two haploid cells fuse, create a cell with a brand new set of DNA that has never been formed before Carry adaptations to survive their environment Determining Relatedness Fossils: ancestral characteristics that may have been lost over time Biochemical evidence: similar protein structures; compare different proteins of organisms; more similar, more closely related DNA evidence: compare introns; the bigger the difference, the longer ago the two animals branched from each other Homologous organs: similar developmental origins, different adult functions Vestigial Organs: structures or organs that seem to serve no useful function Cladistics and Cladograms Cladistics is a classification scheme based on phylogeny System based on the idea that each group of related species has one common ancestor Organisms retain some ancestral characteristics as they evolve and diverge from one common ancestor Cladogram is a branching diagram that resembles a phylogenic tree, but can be used to test alternative hypotheses One common ancestor, branches are drawn to represent different evolutionary processes that took place and the organisms that evolution created More recent the group split, more related they are Monophyletic, paraphyletic, polyphyletic (Look on Wikipedia for more information)

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