FSU BSC 1005 Exam Guide: Viruses and Human Disease by Dr. Hengli Tang Faculty Coordinator: Carolyn Shultz Viruses and Human Disease (Supplement this study guide with pictures from the review/ book to ensure an A) Virus an obligatory intracellular parasite that carries a nucleic acid genome enclosed by a protein coat EnveloWe also discuss several other topics like What is the importance of premack's research with chimps?
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ped viruses viruses that have additional lipid membrane surrounding the protein coat Virions Refers to a physical particle, wheres a virus is a more general term. Also called virus particles. Resolution of a microscope ability to distinguish two objects as separate entities Bacteriophages viruses that infect bacterial cells Micron 1 micron = 1 micrometer; typical range for bacterial and eukaryotic cells Nanometer typical range for viruses Angstrom 1 nanometer = 10 angstrom; molecules are in this range Sources of illumination photons and electrons What is the viral cause of the common cold Rhinovirus What is the viral cause of the flu influenza virus What is the viral cause of warts human papillomavirus 1, 2, 4What is the viral cause of cold sores herpes virus What is the viral cause of diarrhea Enterovirus What is the viral cause of AIDS HIV What is the viral cause of poliomyelitis Poliovirus What is the viral cause of hemorrhagic fever ebola, dengue What is the viral cause of SARS Coronavirus What does TEM do examines the cross section of biological samples SEM scans the surface of biological structures What does CyroEM do ultra-low temperature and quick freezing to preserve the native structure of the virus What does EM Tomography do the CT scan of viruses, with the sample tilted and the microscope stationary. Transmembrane protein a protein that spans across the membrane lipid bilayer Viral receptor a cell surface molecule that is bound by a virus to mediate its entry into host cells Tropism the phenomenon that viruses are capable of infecting certain cell types but not others Endocytosis cellular uptake of materials from extracellular space, using membrane-bound vesicles called endosomesHighly pathogenic avian influenza (HPAI) virus avian flu virus that has crossed over from waterfowl to domestic bird and cases high rate of death in the latter population Virus life cycle: entry includes receptor-binding all the way to membrane penetration Virus life cycle: replication of viral genomes requires the expression of replication enzymes Viral life cycle: assembly and exit requires the expression of structural proteins structure of biological membranes: lipid bilayer has embedded transmembrane proteins structure of biological membranes: barrier that viruses must cross to deliver its genome into the cells 4 possible routes of viral entry pore formation at the cell surface, membrane fusion at the cell surface, pore formation in the endosomes, membrane fusion in the endosomes Nucleic acid a polymer made up of repeating unites of nucleotides; can either be DNA or RNA semiconservative replication during DNA replication, each daughter DNA contains one strand of parental DNA and one strand of new DNA reverse transcriptase the enzyme that uses RNA as a template to produce DNA RNA-dependent RNA polymerase enzyme that uses RNA as a template to produce RNA seven types of viral genes dsDNA, ssDNA, dsRNA, ss(+)RNA, ss(-)RNA, ss(+)RNA/RT, dsDNA/RT why do RNA viruses have a higher mutation rate enzymes used to copy RNA genomes have low fidelity during replication positive-sense RNA directly spells out the code fro protein translationnegative-sense RNA needs to be converted to positive-sense RNA to spell out the code for protein translation Icosahedron a common shape adopted by viruses; characterized by having 20 faces and 3 types of symmetries Packaging signal piece of viral DNA/RNA sequence that is necessary and sufficient for incorporation into virions Metastable state long-lived stable state that is less stable than the most stable state Envelope proteins virus encoded proteins displayed on the membrane surface of the virion RNA secondary structure partially double stranded structures characteristics of an icosahedron 20 faces and 3 types of symmetry; sphere like properties and readily scalable 3 modes of virus assembly self-assembly, chaperones and scaffolds, vision maturation different ways the assembled visions exit from the host cell cell lysis, budding out at the plasma membrane, exocytosis Cytoskeleton a network of interconnected filaments and tubules that extends throughout the cytosol Exocytosis reverse of the endocytosis In vitro outside a body and in cultured cells In vivo in the body of a living organism primary cells directly isolated from organisms, short livedcell lines grow forever but usually are altered from the original cell type BSL-1 no known hazard BSL-2 moderate hazards; lab coats, gloves, biosafety cabinet BSL-3 serious of potentially lethal agents; restricted access, gown shoe over, negative pressure etc. BSL-4 extremely hazardous infectious agents; isolated zone, chemical shower, etc. signal transduction the process of translating ligand-receptor interaction into changes in cellular function or gene expression receptor-mediated endocytosis receptor binding, pit formation, membrane pinching off, acidification of endosomes, receptor recycling, fusion with lysosomes function of a tRNA to bring amino acids to mRNA in an ordered fashion, translating the mRNA code to protein sequence in the process similarities between exocytosis and virus exit require membrane-bound secretory vesicles, travels from center of the cell to the outer edge PAMP pathogen associated molecular patterns pRR pattern recognition receptor; host proteins that detect PAMPs and activate celllular responses Seroconversion the point when antibodies against a virus become detectable in a patient's blood the multiple layers of host defense against infections primary barrier and chemical defense, intrinsic cellular response, innate immunity, adapted immunityexamples of different PRRs toll-like receptors, localized on cell membrane or endosome membranes; RNA helicases, localized in the cytoplasm production of interferons all viral infections trigger the production of interferons action of interferons act through signal transduction pathways and establish an antiviral state in cells RNA silencing antiviral defense mechanism for both plants and animal cells immune memory presence of antiviral antibodies in one's blood is an indication of prior infection by that virus Viral pathogenesis the sum of the effects on the host exerted by virus replication and by the immune response Zoonosis transmission of viral infection from animals to human under natural conditions main portal of entry for common human viruses respiratory tract, GI tract, skin, blood, genital tract three modes of viral infection and circulation liver, heart, nervous system what are Koch's postulates for proving a pathogen is the cause of an infectious disease mosquitos are common vectors for flaviviruses: WNV, YFV, and dengue virus acute infection resolved quickly and survivors gain immunity to subsequent infection chronic infection infection is not resolved by immune system and disease lasts for a lifetime unless treated with drugs influence disease host genetics and geographic factorsrelationship between oncogenic virus and cancer development cell transformation and immortalization; oncogenes and tumor suppressor genes the prion and the prion diseases not a virus, but a subtler agent made of a misfolded protein Syncytium a giant cell with multiple nuclei, resulted from cell-cell fusion between HIV infected cells and uninfected T cells displaying HIV receptors Topical microbicides preparations that are applied either vaginally and/or rectally to prevent sexually transmitted diseases range of deaths greater than 30 million HIV+ people; 1-2 million people die each year of AIDS origin of HIV and the discovery of HIV primate virus transferred to humans difference between X4 (T-Tropic) and R5 (M-Tropic) viruses X4 found in patients of early stage infection while R5 is found in late stage HIV patients 3 modes of sexual transmission for HIV sexual contact, blood borne, mother-child transmission HIV/AIDS disease progression AIDS patients die of opportunistic infections while the CD4+T cells are depleted by HIVinfection HIV life cycle viral entry; reverse transcription; integration; virus assembly, release, and maturation challenges to the successful development of an AIDS vaccine virus is hyper variable because of high error rate of its reverse transcriptase; major targets for HIV neutralizing antibodies are hard to access; target for broadly neutralizing antibodies is unstable Emerging viruses viruses that appear suddenly or suddenly come to the attention of scientists Influenza virus reassortmentco-infection of the same host with two different flu viruses leads to re-mix of the genome segments during viral packaging environmental factors that can influence the emergence of viral diseases weather pattern change; conversion of forests into agricultural grassland; flooding of rice fields human factors that can influence the emergence of viral diseases migration from rural areas to overcrowded, hastily built town at the outskirts of big cities; increased international travel, trade viral factors that can influence the emergence of viral diseases reassortment of influenza virus effective ways of controlling a pandemic quarantine and travel restrictions; identification of virus causing the diseases and transmission route to cut down transmission; development of antiviral drugs and vaccines difference between "seasonal flu" versus "pandemic flu" seasonal flu virus has been with the human population for a while; pandemic flu is typically caused by a new combination of HA and NA examples of mosquito-borne viruses dengue, WNV, yellow feverFSU BSC 1005 Exam Guide: Living with Dinosaurs by Dr. Gregory M. Erickson Faculty Coordinator: Carolyn Shultz Living with Dinosaurs (Supplement this study guide with pictures from the review/ book to ensure an A) Paleontologist someone who studies "ancient organisms" Paleobiology the study of ancient life The first written accounts of dinosaurs were where? China Srcrotum humanum Megalosaur thigh bone; The first proper scientific name given to a dinosaur Reverend William Buckland credited with scientifically describing: the first dinosaur Cuvier Discovered things can and do go extinct and did this by using the Mosasaurus Richard Owen Created the name "Dinosauria" or fearfully great reptiles 1842 Thomas Jefferson considered one of the founding fathers of paleontology Louis Dollo First dinosaur paleobiologist Megalosaurus First valid dinosaur, people were not excited because they were more fascinated with the possibility of 30 foot crocodiles Deinonychus Discovery by John Ostrum in 1964, shifted away from dino's being slow and lumber What started the dinosaur renaissance?Bakker took the idea of the Deinonychus and ran with it; interest in dinosaur research soared What was the first described herbivorus dinosaur? Iguanadon What includes crocodilians, pterosaurs and "dinosauromorphs?" Archosaurian reptiles Archosaurian Reptiles Extinct flying reptiles; -teeth in sockets -erect posture Which of the two relatives is the closest related to dinosaurs? pterosaurs and "dinosauromorphs" 2 Types of dinosaurs Ornithischians "bird hips" Saurischians "lizard hips" Characteristics of: Ornithischians "bird hips" pelvic bones shaped like those of birds; pubis pointed backwards, herbivorous 2 Groups of Ornithischians: Thyrephora + Cerapoda Thyrephora Group "shield bearers", herbivores, bones in skin (Osteoderms) Ankylosaurs "fused lizard" Stegosaurus leaf shaped teeth, olfactory bulbs Saurischians "lizard hips" pelvic like lizards; pubis pointed forward (Ex. T-Rex) Characteristics of: Cerapoda Group (Biggest) spike thumbed iguanodonts, duck bill, bone heads, horned dinosaurs Cerapoda Subgroups: (2) Ornithopods + Marginocephalia Heterodontosaurstwo different kinds of teeth shaped like mammals, sexual dimorphism Advanced Ornithopods tail teeter-totted, criss cross back and tail tendons Hadrosaurs duck bill, dental batteries Dental Batteries in Hadrosaurs hundreds of tightly adjoining teeth, the harder tissue, enamel was on one side so that the teeth were self sharpening Segnosaurs only herbivorous theropod Birds evolved from... Velociraptor; Maniraptoran Theropods How long ago did dinosaurs go extinct? 65.5 million years ago What do we use to know how old dinosaurs are? What does it turn into? Uranium 235, Lead What is the amount of time it takes for half of the original material to break down? Half-life What was the climate in the age of the dinosaurs? -The world was warmer -no ice at the poles -like FL in middle latitudes Ceratosaurs aka "Horned Lizard"; Type of theropod; gap between premaxilla and maxilla; cannibalistic; slow growth tissue like a crocodile Osteoderm bony bumps on skin similar to those of alligators (armor on the skin) What caused the continents to move? Plate tectonics (volcanic seafloor spreading in the oceans) What kind of animals were dinosaurs? Land or water? Land (terrestrial)Crocodile (deinosuchus) -Picture that looks like a dinosaur head is actually what? (pg 25) -also fed on dinosaurs Biggest bite force of giant crocodile was what? 3700 lbs; deinosuchus crocodile What was the Loch Ness Monster? Plesiosaurs When did mammals appear? Time of the dinosaurs Time of the dinosaurs What are the best fossils to use and are also the #1 indicator in the field? Trace fossils: tracks, eggs, bite marks, coprolites(feces) What do dinosaur tracks tell us? Dinosaurs didn't drag their tails In what kind of rocks are dinosaur fossils found? Sedimentary rocks Can you find dinosaurs in FL? Where can you find the closest? No, in Georgia What size were the first dinosaurs? Small How we know about the brain size of some dinosaurs? Endocasts Definition of Endocasts formed by sediments that infilled the brain cavity during the fossilization process and became solidified (Stegosaurs) Paleontology was founded solely in what? Geology Do we know the sex of dinosaurs? No Sexual Dimorphism there were considerable size differences between the sexes; the larger size had long caninesHow many dinosaurs do we know the color of? One We know more about what dinosaur than any other? Duck Bill How do we know more about duck billed dinosaurs than any other? we have remains of eggs, nestlings, embryos, stomach contents, mummified specimens and coprolites What is Over splitting? naming more species than really exist Is the Hadrosaur's nose on top of its head like a snorkel? No Finite element models computer modeling showing the biomechanical performance of the domes ex: head on collision or flank butting model in Marginocephalia Found eggs near ___. Thought ___ stole the eggs. But actually it was their eggs. Protoceratops, oviraptor The dinosaur _______ boss, was said to have a base that was for an _______ pachyrhinosaur, enormous horn How long were Diplodocids? 140ft (longer than Ruby Diamond) Apatosaurus were also named __ because they thought they were different. This is called what? Brontosaurus, over-splitting (named Apatosaurus because of name priority) ________ was the tallest dinosaur at __ ft and is taller than Ruby Diamond Sauroposeidon, 56 Dinosaur with nostrils on top of head? Sauropod Dinosaur that showed crocodile remains in stomach? CeleopisusWhich dinosaur had its skeleton blown to smithereens in WWII when the British bombed the museum in Germany? Spinosaurus Coelurosauria Nastiest dinosaurs Ornithomimosaurs Fastest dinosaur like an ostrich Segnosaurs Dinosaur that was the only herbivorous theropods and had scissor hands What were the smartest dinosaurs? Troodontids Encephalization Quotient (EQ) a measure of brain size relative to body mass Theorized what a dinosaur would look like today if it had not gone extinct=an alien (pg 79) Dinosauroid What was wrong with the first drawing of a T Rex? Too many claws and its tail was on the ground T Rex's best sense? Smell because of huge olfactory bulbs T.rex had a great sense of smell which we know because of the _______. Endocasts This dinosaur was cannibalistic, could only amble (not run), and acted like a scavenger and predator(more this than scavenger); stereoscopic vision T Rex Are T Rex's loners or gregarious? Gregarious; evidence shows they moved in herds What did the 1960s signal? The Dinosaur Renaissance Dinosaurs metabolism was a blend of what animals? Mammal and reptile Growth rates of dinos?-grew faster than reptiles -appear to have grown like marsupials What percentage of life died 65.5 million years ago? 40% to 80% What were the 3 theories of dinosaur extinction? -volcanoes -lowering in sea levels -asteroid (gulf of mexico) What did the theories not explain? why birds, mammals, crocodiles, and frogs were not killed What was the first bird that flew like a dinosaur? Archaeoptryx= "ancient wing" Theropod shares hollow bones with birds True/False- Dinosaurs had feathers True At 7 oz, _______ were the smallest dinosaurs Raptors How much did the smallest dinosaur weigh? 7 oz Dinosaurs have _______ which is similar to a bird hollow bones Paleontologists estimated the biting force of Allosaurus with ______. computer modeling What rock can reveal dinosaur bones because of the lack of vegetation? Rocks from badlands How long ago did dinosaurs live? 238 million years ago (Mesozoic Era)FSU BSC 1005 Fall 2016 Exam: Plants and People by Dr. George W. Bates Faculty Coordinator: Carolyn Schultz Plants and People (Supplement this study guide with pictures from the review/ book to ensure an A) State the characteristics of green plants. ∙ Plants are green (because they contain cholorophyll)— photosynthesis. ∙ Plants cannot move because each plant cell is surrounded by a rigid cell wall. ∙ Method of reproduction is different (plants make flowers, fruits, seeds, or in the case of mosses and ferns, make spores). How are organisms made? ∙ Binomial system (genus, species). How are organisms classified? ∙ On the basis of their evolutionary/genetic relatedness. The first organisms to evolve. ∙ Bacteria Life first appeared when? ∙ 3.5 billion years ago. Photosynthesis evolved when? ∙ 3 billion years ago Multicellular organisms evolved when? ∙ 1.5 billion years ago The more “___” organisms evolved from bacteria. ∙ “complex” Green land plants evolved (separated from other groups) about “___” billion years ago. ∙ “1” Animals are more closely related to” ____ “then they are to” _____.”∙ “Fungi” ∙ “Plants” All living things are composed of” _____.” ∙ “cells” The basic unit of life is the “________.” ∙ “cell” Each cell is surrounded by a “_____.” ∙ “Cell membrane” Each cell contains a “_____” and a “____.” ∙ “Nucleus” ∙ “Cytoplasm” Plant cells have all the components found in “___” cells, but in addition have a “_____” on the outside of the cell membrane. ∙ “animal” ∙ “cell wall” Function of the cell wall. ∙ Provides the plant cell with structural strength and rigidity. Site of Photosynthesis ∙ Chloroplast Chemical reaction of photosynthesis. ∙ CO2 and water are converted into sugars plus oxygen by means of light energy. What is the reaction that makes life possible? ∙ Photosynthesis Carbon cycle ∙ Carbon from the atmosphere passes to plants and then to animals then back to the atmosphere. How do animals obtain their carbon? ∙ Eating Plants How do animals get their energy? ∙ By digesting plant materials, breaking them down into CO2 + water through the process of respiration.What is the function of the xylem? ∙ Transports water from the roots to the leaves What is the function of the phloem? ∙ Transports sugars from the leaves to all the parts of the plant that aren’t photosynthetic. Parts of the plant that aren’t photosynthetic? ∙ Roots ∙ Interior parts of the stem ∙ Fruits ∙ Flowers Transpiration ∙ The movement of water from the roots to the leaves and then out of the atmosphere. Transpiration’s relation to photosynthesis ∙ In order to carry out photosynthesis, a plant needs to open its stomate to exchange gases. ∙ It turns water and carbon dioxide into glucose. ∙ Opening the stomate through causes of the loss of water. ∙ This evaporation causes water to be pulled up from the soil (transpiration). Guard cells. ∙ Regulate transpiration by swelling or shrinking to open or close the pore. Process of guard cells ∙ When the cell has plenty of water, they swell and open the stomate allowing CO2 into the leaf and allowing the water to escape when the soil is dry, they shrink, closing the stomate when they are closed, the plant loses much water, photosynthesis stops. Location of guard cells ∙ Surrounds the stomate Stomates ∙ Special pores in the leaf surface ∙ Vital in restricting water lossPlants restrict water loss by having a waxy layer on the surface of the leaf and allowing CO2 uptake and water release only through “____.” ∙ “Stomates” Cellulose ∙ Molecule in cell walls that provides most of their strength ∙ Composed of chains of sugars that are assembled into rods that are highlight resistant to degradation (resistant to being broken down). Basic Plant Parts ∙ Shoot ∙ Stem ∙ Leaf petiole ∙ Shoot tip ∙ Lateral bud roots ∙ Root tips Stem ∙ Above ground part of the plant. ∙ Consists of the stem ∙ Branches and leaves Leaf petiole ∙ Stalk that attaches each leaf to the stem Shoot tip ∙ Patch of tissues located at the tip of the shoot. ∙ Where new cells are formed (cell division). ∙ Where most of the growth takes place. Lateral bud ∙ Located at the base of each leaf. ∙ Where the petiole connects with the stem. ∙ Dormant shoot tips that when activated to grow will form a branch which is a new shoot system. Lateral bud roots ∙ Below ground portion of the plant. Root tip ∙ End of the lateral bud root.∙ Where cell division and root growth take place. Growth in length is due to “____.” ∙ Cell division is in the shoot and root tips. Plants that live more than one year are called “____.” ∙ “Perennial plants” “______” grow in width by means of cell division in the body of the stem and roots. ∙ “Perennial plants” Growth in length is due to “___” in the shoot tip and root tips ∙ Cell division Shoot tip ∙ Makes the cells of the shoot bud ∙ Leaves ∙ Lateral buds and flowers Modified shoot tip ∙ Flower Basic flower parts ∙ Pistil with stigma ∙ Ovary and ovules ∙ Stamens with anther ∙ Filament and pollen Egg ∙ Female reproductive part Ovule ∙ Where the egg is produced Sperm ∙ Male reproductive part Pollen ∙ Where the sperm is produced Pollination ∙ Transfer of pollen to the stigmaFertilization ∙ Fusion of the sperm and egg to make the next plant generation. After “____” the egg becomes the embryo, the ovule becomes the seed, and the ovary becomes the fruit. ∙ “Fertilization” After fertilization, the egg becomes the “____.” ∙ “Embryo” After fertilization the ovule becomes the “_____.” ∙ “Seed” After fertilization the ovary becomes the “_____.” ∙ “Fruit” Parts of the seed (4) ∙ Seed coat ∙ Embryo ∙ Endosperm ∙ Cotyledons What provides the embryo with nutrients? ∙ Endosperm Modified leaves that also store nutrients for the embryo. ∙ Seed coat Ovule grows and develops into the seed, which contains a plant “____.” ∙ “Embryo” Endosperm ∙ Patch of tissue that surrounds the embryo ∙ Storage tissue that is used for growth of the young seedling Embryo consists of a root-shoot axis bearing two fleshy leaves called the “____.” ∙ “Cotyledon” The function of the flower is to ensure that “___” occurs. ∙ Pollination Features of wind pollinated flowers∙ Petals ∙ Small or absent ∙ Lots of pollen produced ∙ Large stigma Animal-pollinated flowers produce “____” and “_____” ∙ “attractants” ∙ “rewards” Attractants ∙ Colorful petals and scents Rewards ∙ Sugary nectar and pollen Features of flowers that are pollinated by bees ∙ Blue and yellow colors ∙ Sweet odors ∙ Broad open surface or petals ∙ Gives them a place to land so they can sip nectar The colorful spots and stripes on the flowers are cues to help the bee find “_____.” ∙ Nectar Features of plants that are pollinated by flies ∙ Flowers are reddish brown ∙ Release of odor of rotting meat ∙ Draws pollinator to odor, come and find nothing to eat and leave, only to be attracted to another nearby plant, bringing pollen with them. Features of flowers that are pollinated by bats and nocturnal animals ∙ Flowers are open at night ∙ White or dull colored ∙ Have heavy musty/fruity odors ∙ Bats feed on both pollen and nectar ∙ Moths only use nectar Fault or self-pollination ∙ Genetically uniform offspring Flowers are designed to promote “____.” ∙ “Cross-pollination.”Cross-pollination ∙ Increases genetic variability Function of the fruit ∙ Promotes seed dispersal Purpose of fleshy fruits ∙ Intended to be eaten by animals so that the seeds will be dispersed with the animal feces Purpose of dry fruits ∙ Adapted for seed dispersal by animals or by wind or water Dry fruits ∙ Clinging fruits like burrs ∙ Collected by animals like acorns Algae ∙ Simple photosynthetic ∙ Aquatic organisms Plankton ∙ Organisms that live ∙ Suspended in water Phytoplankton ∙ Photosynthetic plankton Importance of phytoplankton in the ocean ∙ Bottom of the food chain ∙ The ultimate source of food for all the animals in the ocean ∙ Produces 30% of the oxygen in the atmosphere Red tide ∙ Blooms ∙ Potentially toxic marine phytoplankton Red and brown algae ∙ Multicellular photosynthetic organisms living in the ocean ∙ Not classified as plants but are in the kingdom Protista ∙ Harvested commercially for their cell wall materials∙ Used for everything from paint and cosmetics to beer and toothpaste “_____” are in the plant kingdom and are the progenitors of land plants. ∙ “green algae” Plants first invaded land, when? ∙ 500 million years ago Earliest land plants ∙ Mosses Moss ∙ Lacks roots/ leaves ∙ Have no xylem or pholoem ∙ Have internal fertilization Internal fertilization ∙ Important adaptation for dry land When ferns and their relatives evolved. ∙ 400 million years ago Ferns ∙ Have xylem and phloem stomates, roots, and leaves. ∙ Reproduce by alternation of generations Alternation of generations ∙ A spore-forming version of the plant makes spores, the spore grows into plants that makes gametes (eggs and sperm) and fertilization results in more plants of the spore forming type (all land plants) Oil and natural gas are derived from the remains of “____” and “____” living in the shallow seas hundreds of millions of years ago. ∙ “Algae” ∙ “Plankton” Coal deposits ∙ The remains of ferns and their relatives living hundreds of millions of years ago. Gymnosperms∙ Cone-bearing plants Major innovation in cone-bearing plants ∙ Seeds and pollen ∙ Allowed plants to reproduce in the absence of water (dry land) pollen ∙ Carried by wind ∙ Delivered the sperm cells directly to the female structure where the egg was produced ∙ Have ovules, seeds, and pollen (but not fruit or flowers) Evolutionary origin of seeds ∙ Instead of shedding their spores as ferns do, cone-bearing plants retain their spores ∙ Surrounded by tissue of the parent plant (called the ovule) Cone-bearing plants ∙ The ovules form on the surfaces of the scales that make the cone ∙ First appeared in fossil records 350 million years ago ∙ Dominant land plants 250 million years ago Conifers ∙ Most important and numerous cone-bearing plants ∙ Pines, spruces, firs, redwoods, etc…. Cycads and ginkgos ∙ Less numerous cone-bearing plants ∙ Predominant land plants ∙ During the age of the dinosaurs Stands of conifers ∙ Cover large parts of the earth’s surface ∙ Particularly in northern latitudes Conifers ∙ Accounts for most wood production % of harvested wood that is used for production of paper ∙ Approx. 50% Paper ∙ Purified cellulose pressed into sheetsEvolution of flowering plants ∙ Ovule became surrounded by a layer of tissue called the ovary Ovary ∙ Layer of tissue surrounding the ovule Flowering land plants ∙ First appeared 150 million years ago but did not become numerous until 100 million years ago. Corn, wheat, rice, and potato ∙ Crops that collectively account for 75% of the calories in the human diet Corn, wheat and rice are all “_____.” ∙ “Grasses” (cereal) Part of corn, wheat and rice that we consume ∙ Fruit and seed The “____” is the part of the seed coat that we consume, “____” is the embryo and the remainder is the “____” ∙ “Bran” ∙ “Germ” ∙ “Endosperm” “____” and “____” in a cereal are mostly in the bran and germ. ∙ “Protein” ∙ “Vitamins” The “___” in a cereal is mostly carbohydrates (starch) ∙ Endosperm White flour ∙ Made from seeds from which the bran and germ have been removed Whole-wheat flour ∙ Contains the entire seed and is nutritionally superior to white flour Rice, wheat, and corn ∙ Low in protein but have sufficient protein for human nutrition although that protein is low in quality.Potatoes ∙ Contain insufficient protein for human nutrition Beans ∙ High in good-quality protein Vegetarian Diet ∙ Must include a range of plants but especially beans for protein and cereal grains for carbs Crop domestication ∙ Began simultaneously at different places around the globe 8- 10 thousand years ago, as soon as the Earth warmed after the last ice age Centers of plant domestication ∙ Middle east ∙ Central America ∙ South America ∙ The Andes ∙ China Wheat ∙ Crop domestication began in the middle east Corns and beans ∙ Crop domestication began in central and northern south America Potato ∙ Crop domestication began in the andes Rice ∙ Crop domestication began in China The earliest crop domestication involved the unintentional selection for: ∙ Loss of natural seed-dispersing mechanism ∙ Reduced seed coat thickness ∙ Greater seed of fruit size Early agricultural innovations ∙ Irrigation∙ Development of the plow ∙ Three-crop rotation system Three-crop rotation system ∙ Replaces soil nutrients needed by plants Plants need a range of “____” nutrients. ∙ “Mineral” Two mineral nutrients most readily lost from the soil ∙ Nitrates and phosphates Bacteria in the soil or living in the roots plants of the pea family ∙ Can convert nitrogen gas in the atmosphere to nitrate Used by plants in building proteins ∙ Nitrate How animals get nitrogen ∙ By eating plants; digest proteins in plants and convert them into animal proteins Nitrogen cycle ∙ bacteria in the soil converts nitrogen gas into nitrate > plants absorb through soil and use to build proteins > animals eat plants and digest proteins to convert into animal proteins Practiced in most modern agriculture over crop rotation ∙ synthetic fertilizer is applied to fields to replace the nutrients that were used up by the previous year's crop “___” for fertilizer is chemically synthesized, “____” for fertilizer are mined. ∙ “Nitrates” ∙ “Phosphates” Responsible for increasing crop yields in the last 100 years ∙ Genetic improvement of crop plants through selective breeding ∙ Mechanization and the use of fertilizers and pesticides Problems with modern agriculture ∙ Fertilizer and pesticide pollution of rivers and lakes ∙ Top soil loss due to repeated plowing ∙ Growing shortages of water∙ Genetic uniformity Genetic uniformity ∙ Facilitates plant diseases FSU BSC 1005 Exam Guide: Synthetic Biology by Dr. Steven Lenhert Faculty Coordinator: Carolyn Shultz Synthetic Biology (Supplement this study guide with pictures from the review/ book to ensure an A) synthetic biology a field of science and technology that seeks to recreate biological functions synthetically, as well as design and construct novel functions based on biological principles. molecular machine a collection of molecular components which work synergistically to carry out a particular function. emergent properties new properties that emerge from collections of components deoxyribonucleic acid (DNA) a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms with the exception of some viruses. proteins organic compounds made of amino acids arranged in a linear chain and folded into a globular form. lipid hydrophobic or amphiphilicsmall molecules. nanometer one billionth of a meter protein folding the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil. biological membrane a lamellar sheet in a biological system containing amphiphilliclipids and forming a hydrophobic barrier, for instance around the cell or organelles. flagellar motor a molecular motor in certain prokaryotic and eukaryotic cells that functions in locomotion by actively rotating a flagellum.Brownian motion thermally driven movement at the molecular level caused by bombardment from neighboring atoms and molecules. kinesin a protein that has the function of transporting materials to various locations inside a cell, similar to how a train transports cargo. biomaterials materials existing in biological systems, or generated synthetically in order to interact with biological systems. DNA nanotechnology a branch of nanotechnology which uses the unique molecular recognition properties of DNA and other nucleic acids to create designed, controllable structures out of DNA. central dogma of molecular biology the idea that genetic information flows from the DNA sequence, to the RNA sequence to the protein sequence. Polymerase Chain Reaction (PCR) a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence fluorescent proteins proteins that are fluorescent, or absorb and emit light at different wavelengths or colors. genome the entirety of an organism's hereditary information. nanotechnology The application of nanoscience in order to control processes on the nanometer scale, i.e. between 1-100 nm. Moore's law a trend in the history of computer hardware manufacturing where the number of transistors per unit area double every 18 months. nanomaterials materials that are structured at the nanometer scale, which often results in new material properties that differs from the bulk properties. antibioticsa substance or compound that kills bacteria or inhibits their growth DNA sequencing methods for determining the order or sequence of the nucleotide bases (A, T, C, and G) in a molecule of DNA. tisssue engineering an interdisciplinary field that applies the principles of engineering and life sciences toward the development of biological substitutes that restore, maintain, or improve tissue function or a whole organ pharmaceutical drug any chemical substance intended for use in the medical diagnosis, cure, treatment, or prevention of disease artifical intelligence the intelligence of machines and the branch of computer science that aims to create it. ethics a branch of philosophy that addresses questions about morality —that is, concepts such as good and evil, right and wrong, virtue and vice, justice, etc. sustainablility the capacity to endure. In ecology, the word describes how biological systems remain diverse and productive over time. natural molecular machines converting sunlight into useable energy (photosythesis), self-replication of DNA and cells, dynamic camouflage, and directed molecular transport are all known biological factors made possible by ________ (traveling back in time is NOT) example of emergence the ability for billions of transistors in a computer to hold a program capable of beating the world chess champion at chess is an 2 nanometers wide a double stranded DNA molecule is... self-replication one example of a biological function that results in exponential growth of products such as DNA and cells, which synthetic biology seeks to recreate synthetically is vegetable oilan example of a well known commercial application of biological lipids Brownian motion Flagellar motors, kinesin motors, ATP synthase, and DNA poymerse are examples of machines that operate at a size (and energy) scale where _______ is considered in understanding its function (Cars do NOT) kinesin a molecular machine that has been shown feasible as an ATP powered molecular transport system for reagents in "smart dust biosensors" central dogma of molecular biology the ability for protein engineers to produce proteins of an arbitrary sequence simply by changing the DNA sequence of an organism (such as E. Coli.) biomaterials DNA, insulin, wound dressings, and implants are examples of....(Plutonium typically is NOT) applications of synthetic biological membranes studying natural membrane function in more controlled environments, drug delivery, gene delivery, and biological sensors are examples of....(thermal insulation in nuclear reactors is NOT) insulin a pharmaceutical protein used ot treat diabetes that is widely produced semi-synthetically using recombinant DNA technology polymerase chain reaction (PCR) the ability for us to read, write, and synthetically amplify DNA sequences is largely made possible by the method known as synthetically a living cell cannot yet be made completely ______ (without the use of natural biological systems- not counting the person who makes them) engineered fluorescent proteins are widely used in biological research for observing the location of proteins in living cells cell membrane a completely synthetic genome was recently inserted into a cell which was grown in culture and found viable. which of the following aspects of the cell: DNA, genes, nucleic acid sequence, and genetic info was enginerred synthetically in that technological feat. its ____ _______ was NOTrealistic type of nanotechnology computers, nanomaterials, nanostructured surfaces of medical implants, and scanning tunneling microsopy are currently viewed as a _________. (self replicating nanorobots are NOT) nanomaterials Muckminsterfullerene (C60), carbon nanotubes, nanoparticles, and quatum dots are examples of _____ (bulk carbon is NOT) clinical tissue engineering trials skin, cartilage, bone, bladder, are all tissues being tested in ______ (Brain, to our knowledge, is NOT) DNA sequencing technologies in medicine gene expression profiling, personalized medicine, improved diagnostics, and gene therapy are all currently feasible applications of ______ (eternal life extension is NOT) human ethics strongly influence what technologies will/will not be developed, as well as the laws that govern/don't govern them. (Technical feasibility is less influenced) sustainability of life improved energy production, reduction in wasted energy, improved food production, and improved monitoring of climate change are ways in which synthetic biology has potential to contribute significantly to the ________ as we know it on earth. (reduction in biodiversity on the planet is NOT) artificial intelligence beating the world chess champion at chess, beating ta world scrabble champion at scrabble, beating a Jeopardy champion at Jeopardy, and recognizing human speech at a practical level are all achievements that have been demonstrated by fluorescent proteins were originally discovered in the bioluminescent (light producing) jellyfish species Aequorea Victoria biomaterials the exsistence of funcional compounds in nature serves as proof and inspiration to scientists that these _________ can be made lipidsalthough water is considered the solvent of life, ____ can be considered an organic phase where a variety of non-polar molecules tend to aggregate and interact DNA nanotechnology The field of ____ ______ has reached a pint where such complex structures can be designed and built that it is sometimes referred to as DNA origami genome One approach being taken towards the development of a synthetic cell is to synthesize an entire ______ that contains all of the DNA that a cell needs to reproduce and survive Polymerase Chain Reaction (PCR) The method for making ____ _____ _____ function is not to reconstruct the entire protein machinery needed to denature (structure change caused by external stress or compounds) the DNA and polymerize it, but rather to find one polymerase (the natural protein used to replicate DNA) that is robust enough for the reaction to be performed at elevated temperatures, where DNA strands spontaneously denature (i.e. melt or sperate)