Bio1100 notes

chap01 The Science of Biology

Chapter 1: The Science of Biology

deductive Hypotheses should be deductive: make predictions (behavior lab)? kingdom_Bacteria Purple sulfur bacteria do not use water to reduce -> O2, hydrogen sulfide -> sulfur. organiz-population Sandhill cranes. homeostasis 98.6 F=37 C. scientific proving: round earth. Math -> theorems. organiz-cellular Matter: has mass and occupies space.

	E: 1=e 1=e 1=b            17=a 18=c 19=f 20=f
	Q: 1=a 1=c 1=b             9=d 10=c

chap02 Evolution and Ecology

Chapter 2: Evolution and Ecology

Darwin Beagle 1831(22)-1836; 20 years. Darwin_monkey John Scopes Tennessee teacher 1925 law: William Jennings Bryan/Clarence Darrow finch_diversity BBC-LifeOfBirds/1.3_TheInsatiableAppetite/#33:40 Title 3 chap 7 Woodpecker finch -> 36:05 Crow On left: tree finches (vegetarian has parrot-like beak; buds) On right: ground (cactus finch fruit and flowers) Santa Cruz in middle, with airport. Geospiza/Tribulus SEEDS PUNCTUREVINE finch_evolution Cactus finch is G. scandens; G. difficilis is sharp-beaked Tiaris obscura (Dull-colored Seedeater) closes relative to Galapagos finches. fossil 2,00kg=4400 pounds. galapagos 600 miles (1000 km) west of Ecuador. Cactus finch is a ground finch but eats fruits & flowers, not seeds. population_progression Malthus Essay on the Principle of Population in 1798. voyage BBC-Galapagos/#10:20 Blue-footed Booby diving; 14:30 Marine Iguana; 30:30 Galapagos Hawk ===

	6e post
	1=T  2=F?
	6=E  7=D  8=C  9=A  10=E
	         12=E 13=B

chap03 The Chemistry of Life

Chapter 3: The Chemistry of Life

pH Revu hydrophilic. Mole=6.02×10²³. elements First play elements Hydrogen isotopes: protium, deuterium, tritium - lookup radioactive half-life. water hydrogen⁺ ion actually Hydronium H₃O⁺ cohesion PAPER CLIP. Sonar to sense objects; territory. Concave meniscus: water molecules attract those of graduated cylinder; capillary to 14 cm for .2 mm tube. bond-ionic Prefix a/an/anti = not, negation: apathy, anonymous, anti. Anode is where anions move to: - in battery (current flows in); + in gel electrophoresis. electrons Orbitals: spdf; 1 Orbital holds 2 electrons. buffer Review: HCO₃^- has lost H⁺, so H₂CO₃ is an acid. bond-hydrogen δ delta charges

	Pre 1=B  2=A!  3=D  4=B?  5=A

chap04 Molecules of Life

Chapter 4: Molecules of Life

carbohydrate-chitin BBC-LifeInTheUndergrowth/1.2_TakingToTheAir/#42:50 17-year CICADA (play TakingToTheAir) exoskeleton (drum-like membranes: tymbals) brood XIII 2007, 1969 after 13 years (2003); brood X 2004 nitrogenous-bases Methylation of uracil produces thymine. carbohydrate-lactose Lactose: glucose + galactose carbohydrate-cellulose TOILET PAPER: TURGID cellulose - POSTPONE to ch05/cell_wall.html sucrose High fructose corn syrup: processed by liver, not insulin -> triglycerides (fats) dehydration Dehydration also condensation. fats MOLYMOD: double bonds; natural peanut butter (no stabilizer - oil will separate)/potato chips: trans fat/omega-3 sugar Fructose another monosaccharide. 6epost: 1=a 2=d 3=c 4=d 5=c 6=t 7=t 8=b 9=c 10=a 11=a 12=a 13=c 14=d 15=F 16=T? 17=b 18=A 19=d 20=a

chap05 Cells

Chapter 5: Cells

prokaryotic Bacterial cell wall: peptidoglycan cell-animal Centrosome contains a pair of centrioles. Plant centrosomes not organized as centrioles. cilia Cilia in trachea epithelial cells of respiratory tract diffusion KOOLAID diffusion ER "Within cytoplasm" "little net". membrane_proteins Cholesterol: testosterone, progesterone, estradiol. cortisol, aldosterone. Low-density lipoprotein (bad LDL) has more Cholesterol. Mosaic: creating images with pieces of glass, stone, tile. cell_wall TOILET PAPER: TURGID cellulose; middle lamella is pectin heteropolysaccharide; also lignen basal_body Basal body has 9 triplets of microtubules. cells Ratio decreased from 3(left) to 1/3-1/4(right). Radius=line from center to perimeter; diameter. cytoskeleton Fiber: bundles of polymers or chains; no secondary structure. sodium-potassium_pump ATP discussed in chap 6. osmosis RAISIN/GRAPES/SALT: 2 cups/chopsticks; drink from a lake or an ocean?

	6ePost 1=C? 2=d  3=d  4=d  5=b  6=c  7=d  8=d  9=b 10=c
	      11=F 12=F 13=T 14=B 15=F 16=T 17=F 18=F 19=T 20=F
	      11: Detoxification occurs in peroxisome.

chap06 Energy and Life

Chapter 6: Energy and Life

active-site Lysozyme in tears and saliva kill bacteria: hydrolize glycosidic bonds in peptidoglycan. catalysis-activation Catalytic converter: reduce emissions (nitrogen oxide, CO) oxidize unburnt hydrocarbons to CO₂ + H₂O; ceramic coated with platinum. energy Potential energy transform is metabolism. energy_flow Peromyscus leucopus/maniculatus has bigger ears, on wheat? entropy Heat: steam engine example. enzyme_allosteric Repressed in upper diagram. enzyme_optimal Trypsin produced in pancreas; 40°C = 104°F; body temp is 37°C. reaction Diagram from ch04/dehydration.html exergonic must first break bond!

	6ePost 1=a  2=a  3=d  4=b  5=d  6=c  7=d  8=b  9=F 10=T
	      11=F 12=T 13=T 14=T 15=a 16=T 17=a 18=c 19=e 20=a

chap07 Photosynthesis: Acquiring Energy from the Sun

Chapter 7: Photosynthesis: Acquiring Energy from the Sun

Calvin Water released in Calvin cycle (carbon fixation dehydration to 6-phosphoglycerate -> transpiration). light Blu-ray DVD: violet laser (405 nm), not red (650 nm). leaf Meso prefix=middle mezzo-soprano between soprano and contralto. carotenoids BANANA; ORANGE 10-13 carpels. Xanthophylls: yellow carotenoid; Anthocyanin: appear red - blue(pH); sunscreen absorbs blue-green; also "antioxidants": radicals from UV. photosystem Electron donor water shown in right arrow and next diagram. photosynthesis Water released in Calbin cycle (carbon fixation dehydration to 6-phosphoglycerate -> transpiration).

	6ePost: 1=c  2=F  3=b  4=b  5=a  6=F  7=F
	        8=D??? (photosystem act as antenna) 
	        9=a  10=F (NADPH made in Photosystem I)
	        11=b 12=F (1%)?
	        13=F 14=A 15=b 16=b 17=A 18=F 19=d 20=b
	TODO: pigments after leaves

chap08 How Cells Harvest Energy from Food

Chapter 8: How Cells Harvest Energy from Food

energy_cycle Water also released from Calvin cycle. respiration Glucose breakdown is glycolysis, NOT hydrolysis. Cyanide inhibits cytochrome c oxidase. Oxygen is electron acceptor: reduced (gain energy) to water or superoxide radical. glycolysis_steps Glycolysis summary: answers are 6, 2, 2, 2, 3 fermentation Probiotic: Lactic acid bacteria, yeasts and bacilli; colon cancer, cholesterol, blood pressure. BBC-BluePlanet/3.5_SeasonalSeas/#14:10 Giant Kelp/bryozoans, Otter using rocks to open clams. Also BRING seaweed

	6e Anim#3 Krebs: 1=d  2=A?
	       #6 PPump: 1=E to outside! 2=c  3=e  d=T  e=F not permeable!
	   post: 1=F! (CELLULAR respiration)  2=T  3=b  4=d  5=F  6=d  7=T  8=F  9=A  10=T
	        11=F 12=d 13=F 14=T 15=T 16=d 17=e 18=B matrix 19=c 20=c inner membrane

chap09 Mitosis

Chapter 9: Mitosis

karyotype Light bands are GC-rich with genes. mitosis-anaphase Centromeres replicate; Review Q: 4 sets of chromosomes. mitosis pro=forward/before; meta=after; ana=up/back telo=end/tail Mitosis review: prometaphase at LOWER RIGHT Animation does not show cell plate:

sexual_life Figure from ch10 chromatin Talk from right to left: nucleosomes coil into solenoids -> loops -> rosettes on scaffolds.

	6eAnim#2 1=c 2=d 3=b 4=F 5=T  
	   post: 1=

chap10 Meiosis

Chapter 10: Meiosis

independent_assortment Assortment exercise: just reverse the last B/b pair:

random_fertilization World population 6.7 B. synapsis Synapsis: homology search. make TENNIS BALL chromosome model

	6eAnim#5 1=e 2=d 3=D (one of each pair of parent cell) 4=F 5=F

chap11 Foundations of Genetics

Chapter 11: Foundations of Genetics

punnett_square Exercise: ESP genetics/002/mainframe48: 1/2 design_1 WASABI(horseradish root) or roasted peas. assortment Review

also in ch10. bloodABO Exercise:

does not drag? just do manual. Donated blood contains only RBC, no plasma.

dihybrid Exercise:

tall, yellow and short, green?!? aneuploidies XYY: metaphase II nondisjunction; Down: epicanthic fold; 2ndary sex traits: pear/apple. environmental BBC-PlanetEarth/3.1_GreatPlains/#12:40 Arctic Fox raids nest, buries egg (photoperiod) nondisjunction ADD figure for meiosis II nondisjunction; use exercise to illustrate. pea Pisum sativum Fabaceae have 1 carpel; 1 standard/banner, 2 wings, and 2 petals - keel.

	7=C Turner XO  9=B Klinefelter XXY  17=A chromosomes  18=C sex-link

chap12 DNA: The Genetic Material

Chapter 12: DNA: The Genetic Material

Franklin 572.8092 FRA (Nichols) Secret of Photo 51: 18:00 Wilkins uses condom 26:30 A and B forms 28:30 Watson/Crick initial model 37:00 Aaron Klug explains Photo 51 Watson/Crick: B form (wet), Franklin worked on A form, ovarian cancer 37; 2 mi S. of Gurnee I94 off Buckley Rd. polymerization This diagram shows just 1 of the 2 old strands! mutations DELAY THIS AFTER CHAP 13. TODO: use 12_11.jpg when corrected. transposition Jumping genes. replication DNA polI removes primer ZIPPER fannypack: leading strand demo; holoenzyme

chap13 How Genes Work

Chapter 13: How Genes Work

translation ESP genetics/005/mainframe108: NO E site on ribosome? ribosome Aminoacyl, peptidyl. tRNA ESP genetics/005/mainframe107? transcription Do not show

promoter/sigma factor not in figure.

	6e post
	1=a  2=F  3=d  4=c  5=a
	6=d  7=b  8=c  9=a  10=b
	11=d 12=b      14=c
	               19=c

chap14 Gene Technology

Chapter 14: Gene Technology

golden Phytate (storage form of phosphorus; inhibits iron reabsorption) destroyed by phytase from Aspergillus - skin infections. herbicide Glyphosate (Roundup) inhibits aromatic a.a. such as phenylalanine (contains a ring). vaccine Herpes simplex: oral=cold sores; genital. Cowpox red blisters; vaccine for smallpox (eliminated). Chickenpox still affects children. genetic_steps Vector: agent that transmits disease; vehicle (quantity that has magnitude and direction). applications QH442.2 .C743 2002: Creation#23:30 woman egg donor, Judson's skin cells thru zona pellucida (glycoprotein) - 32:30 QH442.2 .F67 2006: For spares or repairs Virus discussed in chap 19. plasmid Plasmid -> construct BAC; linearised with restriction enzymes -> YAC. electrophoresis Anode: electric current flows into; in battery electrons flow out. PCR Use Taq polymerase, low replication fidelity; Pfu DNA(archae) can proofread, but slower. cDNA Reverse central dogma; shows which genes are expressed; can be expressed in prokaryotic. Reverse transcriptase: HIV discussed in ch19! therapy defective adenosine deaminase gene. insulin mellitus=type 1, juvenile-onset

	Q 1=c  2=c  3=B?!? 4=c  5=d  6=b  7=a  8=c  9=a 10=d

chap15 Genomics

Chapter 15: Genomics

human_genome Structural: centromere, telomere. Microsatellites=simple-sequence repeats used as molecular markers; CG-rich stain light near genes. duplication can also contribute to genome diversity (later). microarray Review: all the alleles - 100,000. genome_similarity BBC-Galapagos/#2:01:15 Pufferfish? Tetraodon=Pufferfish: ray-finned; tetrapods from lobe-finned. Fill stomach w water (air if out of water) Fugu poison tetrodotoxin in organs, skin from bacteria; can be farmed to be non-toxic.

chap16 The Revolution in Cell Technology

Chapter 16: The Revolution in Cell Technology

dolly Starve both cells to synchronize cell cycle. Large offsporing syndrome due to genomic imprinting: methylation turns gene or regulator off. transplantation QH442.2 .C743 2002: Creation#13:30 Judson paralyzed, skip 21-22:40, 23:30 woman egg donor, skip 27-28:30, zona pellucida (glycoprotein) 32:30 (16 min) QH442.2 .F67 2006: Spares or repairs#5:00 cloning dolly genomic_imprinting methylation can turn off transcription.

chap17 Evolution and Natural Selection

Chapter 17: Evolution and Natural Selection

anatomical-convergent Pterosaur wing: elongated 4th digit. Bird 4 digits; 3 & 4 support wing. anatomical-embryonic NOVA-DarwinNeverKnew/#16:10 Giant armadillo, 18:00 Snake embryo, 18:45 Pharyngeal pouches - inner ear. anatomical-homologous Horse phalanges: 1 hoof beneath Tibia, Tarsus (joint), Metatarsus; 2 useless splint bones? evolution Punctuated equilibrium=cladogenesis (Stephen Jay Gould): fossils show stasis; geographic/allopatric speciation. Gradualism=anagenesis. fossil_whales PBS-Evolution/2.2_change/#11:20 ->14:10 Basilosaurus (aquatic) had leg bones, but Sinonyx was wolf-like mammal 50 MYA. Anthracotheres hippopo-like artiodactyl even-toed. Baleen embryos had teeth, resorbed. Toothed whales: dolphins, Orca, Sperm, Narwhal. hw-conditions Null hypothesis predicts no difference. hw-mutations Overall mutation rate 10 billion. hw-selection NOVA-DarwinNeverKnew/#31:30 Rock Pocket Mouse light/dark fur isolation-behavioral chipping, tree, or field sparrow? isolation-mechanical Copepods use 5th legs to place spermatophore. isolation-temporal snowdrops; spring field cricket selection-directional Phototropism should be phototaxis? struggle Myanmar=Burma variation Biston betularia dark form more after Industrial Revolution 18th - 19th century. === This chapter is long!

chap18 How We Name Living Things

Chapter 18: How We Name Living Things

domain-Archaea cell wall polysaccharide, glycoprotein cladogram Archosaurs: thecodonts (cone-shaped teeth socket); snake teeth simply joined to bone; turtle egg tooth. domain-Bacteria Cyanobacteria -> chloroplasts (also fix nitrogen; purple bacteria -> mitochondria Rhizobium=Gram-negative proteobacteria; atmosphere 78% nitrogen, 21%oxygen. Quercus_rubra QUERCUS RUBRA LEAVES, ACORNS. endosymbiosis BBC-BluePlanet/3.6_CoralSeas/#5:30 Coral polyp structure 6:55 Inside corals are Algae ("plants"=Dinoflagellata) 9:15 polyps fight at night

chap19 Prokaryotes: The First Single-Celled Creatures

Chapter 19: Prokaryotes: The First Single-Celled Creatures

HIV also contains protease, integrase; infects macrophages (phagocytes, little damage), later T cells.

chap30 Respiration

Chapter 30: Respiration

chap31 The Path of Food Through the Animal Body

Chapter 31: The Path of Food Through the Animal Body

BBC-LifeOfBirds/1.3_TheInsatiableAppetite/#41:00 European Robin

chap32 Maintaining the Internal Environment

Chapter 32: Maintaining the Internal Environment

chap33 How the Animal Body Defends Itself

Chapter 33: How the Animal Body Defends Itself

BBC-Galapagos/#35:15 Galapagos Sea Lions competing to be beachmaster BBC-LifeOfBirds/1.3_TheInsatiableAppetite/#7:35 Acorn Woodpecker (Clark's nutcracker remember 2K caches pine seeds) BBC-BluePlanet/3.5_SeasonalSeas/#14:10 Giant Kelp/bryozoans, Otter using rocks to open clams QL785 .A656 2003: Animal minds weaver_birds review Canon PowerShot camera

chap34 The Nervous System

Chapter 34: The Nervous System

BBC-LifeOfBirds/3.A_LimitsOfEndurance/#33:30 Brown Tree Snake Nuisance Fish DVD Nuisance Fish DVD QC981.8.G56 G672 2006: An inconvenient truth QC981.G56 G563 2006: Global warning QC791.4 .B688 2002: Bottling the sun TJ808 .E85 2006: The ethanol solution

chap36 Reproduction and Development

Chapter 36: Reproduction and Development

hermaphroditism Hermes=Greek messenger (Roman Mercury); Aphrodite=Venus PBS-ShapeOfLife/2.3_TheFirstHunter/#37:30 , 39:30 Hermaphrodite flatworms perform penis fencing BBC-LifeInTheUndergrowth/1.1_InvasionOfTheLand/#23:00 Hermaphrodite Leopard Slugs mating in midair Bizarre foods: escargot caviar Bluehead wrasse female sex change if terminal males removed: social control sex-determination SRY=Sex-determining Region Y ZW chromosomes in birds; XXY: high FSH, LH; XYY are normal homeotherm BBC-Galapagos/#2:08:50 Blue-footed Booby mating; Nazca Booby eldest chick pushes younger out of nest: sibling rivalry female_organs Other mammals have uterine horns. Clitoris above urethra and vagina, homologous to penis - stimulation. sperm Sperm's centrioles: form spindle for the first zygote division. oogenesis Primary oocytes in prophase I at birth. 300-400 oocytes ovulated in a lifetime; Corpus luteum secretes progesterone. Clomiphene inhibits negative feedback on hypothalamus for Gonadotropins (LH FSH). male_organs Labeling exercise:

epididymis left 2 Seminal vesicles 60% of semen, prostate into urethra, bulbourethral clear mucus: neutralizes acidic urine. Leydig (interstitial cells): secrete testosterone. external_fertilization Bufonidae true toads: poison gland (parotid, tympanum hearing); spadefoot is Scaphiopodidae. Some Rana (true frogs) burrow.

chap37 Populations and Communities

Chapter 37: Populations and Communities

competition Barnacles are arthropods, not molluscs like clams. competitive_exclusion First 2 Paramecium feed on bacteria; bursaria prefers yeast. growth Malthus: geometric progression=Exponential predation Moose 2 large/2 small toes: Order Artiodactyla resource_partitioning Blackburnian orange throat: tips of coniferous/deciduous leaves Bay-breasted: middle Myrtle (Yellow-rumped) lower Cape May high Black Throated Green apex (Yellow warbler nests here) symbiotic BBC-LifeOfMammals/1.2_InsectHunters/#43:20 Lesser Short-tailed Bats capture Wetta; pollinate Dactylanthus symbiotic-commensalism_buffalo BBC-LifeOfBirds/1.3_TheInsatiableAppetite/#43:45 Cattle Tyrant, 46:40 Oxpeckers also eat earwax. symbiotic-commensalism_sea Clownfish protandrous: 26 species/10 anemones. (Ocellaris Clownfish & Magnificent sea anemone in Finding Nemo 3 stripes) symbiotic-ectoparasitism Cuscuta symbiotic-mutualism BBC-LifeInTheUndergrowth/2.1_IntimateRelations/#00:45 Ants protecting aphids from ladybeetle IMAX-Coralfilm/#9:45 Goby/Bulldozer Shrimp; 12:30 coral bleaching. (choose Dolby, #3: Great Barrier Reef) symbiotic-mutualism_acacia Beltian bodies: lipids and proteins. symbiotic-parasitism BBC-LifeInTheUndergrowth/1.2_TakingToTheAir/#20:15 Damaged cabbage attracts parasitoid Parasitoid Wasp; Cotesia Wasp grubs later emerge BBC-LifeInTheUndergrowth/2.1_IntimateRelations/#11:30 Parasitoid wasp oviposits into gall wasp larva; 44:10 Ichneumon wasp ===

chap38 Ecosystems

Chapter 38: Ecosystems

consumers BBC-Galapagos/#10:20 Blue Footed booby fed on by Ghost Crab detritivore 12:40 Gecarcinus quadratus=Halloween crab. cycle_nitrogen Nitrogen 78% atmosphere, 21% O. deep-sea Flashlight fish Photoblepharon steinitzi. deep-vent QL125.6 .V653 2005: Volcanoes of the deep sea 577.799 ALL 2005: (Nichols) Aliens of the Deep 37:00-38:40 (Snake Pit, Mid Atlantic Ridge) black smokers; 1:17:00-1:19:10 shrimp feed on bacteria on crabs; 1:19:20-1:21:30 (Nine North, East Pacific Rise) tube worms symbiotic bacteria Beardworms Vestimentiferans. heterotrophs A beetle elytra? (350,000 species). open-sea BBC-BluePlanet/3.5_SeasonalSeas/#4:50 Phytoplankton; 11:25 Basking Shark filters plankton rain_shadow TENNIS BALL EARTH; Gobi Desert in Asia shallow_waters continental shelf: 20 m, shelf break, continental slope solar Radiation: absorbing energy without direct contact (conduction); convection movement of fluid. Tilt 23.5°=tropics; Naperville latitude=41 deg N, 45 min, 02 sec. ===

chap39 Behavior and the Environment

Chapter 39: Behavior and the Environment

altruistic Meerkats inspection. auditory NOVA-Animals Behaving Worse? Stand up to snakes. cognition BBC-LifeOfBirds/1.3_TheInsatiableAppetite/#7:35 Acorn Woodpecker (Clark's nutcracker remember 2K caches pine seeds) QL785 .A656 2003: Animal minds fixed_action_pattern Ocean stickleback has spikes on belly. imprinting BBC-PlanetEarth/4.1_SeasonalForests/#22:05 Mandarin Ducks nest in tree. Wood ducks jump to join brood by imprinting. intrasexual_selection BBC-Galapagos/#35:15 Galapagos Sea Lions compete to be beachmaster sign_stimulus Geese territorial in breeding season. white-crowned_sparrow Song repeated over; mimics: mockingbird, brown thrasher, gray catbird. === Classical conditioning: Canon PowerShot camera

chap40 How Humans Influence the Living World

Chapter 40: How Humans Influence the Living World

acid_precipitation Kill mycorrhyzae, excess protons release cation minerals from soil. amphibia Wetland loss, acid precip; chytrid soil fungus spread in banana crates: flagellated spores. biological_magnification Poliomyelitis caused by virus, not body lice. FDR 1921 age 39. Malaria and typhus (flea), moderately toxic. Eat SMALL fish, veggies. Osprey? Northern Harrier female are ringtails? 10K fold water-plankton. ethanol Sugarcane, oil palms; celluslose-digesting from termites, also hemicellulose. extinction Nuisance Fish DVD. footprint US footprint (at bottom) 9.7 hectares * 2.47 = 24 acres habitat_loss BBC-Earth/Disc2/#1:24:50 Baobab trees left in Madagascar Lemur primates: grasping fingers + binocular vision. habitat_restoration Liatris pycnostachya? BLAZING STAR. Aldo Leopold. human_population_growth health care, sanitation, education. ozone_hole Lower stratosphere 10 km - 50 km; stratosphere 20 km; In 2000, the 11.4-million-square-mile hole covered an area larger than the United States, Canada, and Mexico combined. PolyChlorinated Biphenyl PCB: coolant, adhesives, paint. === BBC-LifeOfBirds/3.A_LimitsOfEndurance/#33:30 Brown Tree Snake Nuisance Fish DVD Nuisance Fish DVD QC981.8.G56 G672 2006: An inconvenient truth QC981.G56 G563 2006: Global warning QC791.4 .B688 2002: Bottling the sun TJ808 .E85 2006: The ethanol solution


Bio1100 notes	Updated: May 09, 2010.	Peter Chen