Bio1151 notes

Chap 01 Introduction: Themes in the Study of Life

Chapter 1: Introduction: Themes in the Study of Life

hier1-population deer in hier1-community.html? hier2-molecule chlorophyll 4 porphyrin rings: O, N, Mg hier2-tissue epidermal eukarya Order Carnivora posses carnassials: last upper premolars and first lower molars adapted for shearing food in a scissor-like manner. Scientific edison 2K trials carbon filament (platinum did not work) 1879, replaced by tungsten. (argon-nitrogen) (quartz glass/halogen-iodine,krypton,xenon) Electrical Discharge: phosphor coatings: Fluorescent, Mercury/Soduim Vapour ===

	SQ 1=B  2=d  3=a  4=C  5=c
	   6=c  7=c  8=D  9=b 10=c
	        ===  ---

Chap 02 The Chemical Context of Life

Chapter 2: The Chemical Context of Life

element Elements song PENCIL graphite, PAPER CLIP: Al 13. elements Magnesium: bone & teeth, co-factor in enzymes; chlorophyll. atom He atomic number? 2 Mass? 4. Electron cloud and shells. excited Argon atomic number 18: 1s2, 2s2, 2p6, 3s2, 3p6. Since all of its 3p orbitals are filled, it is considered a noble gas. The 3rd principal energy level can also accept up to 5 3d orbitals (3d5), so it can be said that the 3rd "shell" has a maximum of 18 electrons (quantum mechanical model), but 8 electrons (Bohr model) in the 3rd "shell" is stable. shells PENCIL graphite, PAPER CLIP: Al 13; matter: has mass + space; Hindenburg ! H/He balloon , elements. gecko Van de Graaff electrostatic generator: static by chemical reaction. ===

	SQ 1=B  2=a  3=b  4=B? 5=C? 6=B? 7=b  8=a  9=b 10=b

Chap 03 Water and the Fitness of the Environment

Chapter 3: Water and the Fitness of the Environment

surface PAPER CLIP, FORK; sonar; territory; graduated cylinder Clark'swestern grebe crop (Oregon). Fire ants raft cohesion Sequoia sempervirens 112 m, Eucalyptus regnans 150 m ice BBC-BluePlanet/1.2_FrozenSeas/#29:45 Euphausiid shrimp (Krill) scrape algae off ice pH Avogadro 6.02 * 10²³ acid_precipitation Limestone/dolomite basic. ===

	SQ 1=d  2=D  3=B  4=c  5=b  6=c  7=c  8=D  9=C 10=C
	AQ 1=b  2=d  3=a  4=a  5=e
	CQ 1=e  2=a  3=e?

Chap 04 Carbon and the Molecular Diversity of Life

Chapter 4: Carbon and the Molecular Diversity of Life

isomers MOLYMOD. Latin levo and dextro. L-alanine animation warmup. ACT 4B isomers step 4: stru, stru, iden, enan, geom, stru, diff, enan, geom, stru, diff, iden redo functional group figures from LEC ppt isomer-geometric Rhodopsin cis -> trans (such as retinal) isomer-enantiomer Dextro - levo. L-DOPA (derivative of L-tyrosine) treats PD, can cross BBB, converted to dopamine. functional Revu! phosphate valence +3 (3 p electrons) but also +5 (with s orbital electrons?) (-OPO₃^2-) sulfhydryl Cysteine has SH; sulfuric acid is H2SO4. hormones hydroxyl, carbonyl (C is hidden), methyl ===

	SQ 1=d 2=c

Chap 05 The Structure and Function of Macromolecules

Chapter 5: The Structure and Function of Macromolecules

carbohydrate This diagram is starch. monosaccharides Glucose & galactose are stereo isomers. glucose Hydroxyls on 1 & 2 carbons - not geometric no double bond. chitin BBC-LifeInTheUndergrowth/1.2_TakingToTheAir/#1:33:20 Cicadas Every other glucose (beta form) is upside down to its neighbors. cellulose Beta glucose monomers. starch Alpha glucose monomers (stereo isomer at carbon 1). Amylopectin is branched like glycogen. fat-saturated This is stearic acid; fish unsaturated. fat-unsaturated PEANUT BUTTER/POTATO CHIPS: trans fat/onega-3. This is oleic acid found in olive oil. Unsaturated converted to solids by hydrogenation. protein Fibers (actin) have no 2nd structure. amino_acid Only L isomers are found in proteins. ===


	SQ 1=d  2=c  3=A  4=a  5=b  6=a  7=D  8=B  9=B 10=b

Sugars glucose: blood sugar galactose: milk, yogurt fructose: HF corn syrup, fruit, vegetables, not regulated by insulin -> fat; insulin resis; type II diabetes; corn price artificially low D-glucose and L-glucose are enantiomers. D-glucose (dextrose) in living things, left-handed L amino acids.
Carbohydrate loading: deplete glycogen, then carb-rich 3 days b4 event; now no depletion - decreased training.
Lipids: bread contains mono- and diglycerides as “dough conditioners.” Fatty acids in soap (Romans animal fat and wood ashes): hydrophobic tails, carboxyl hydrophilic heads: emulsify oily dirt. Phosphate builders sodium tripolyphosphate (dry detergents) or sodium/potassium phosphates.
Hydrogenated fats may contain trans-fats: LDL low-density lipoproteins transport cholesterol from liver to tissues.
Natural peanut butter: no stabilizer; oil separates.
transthyretin: plasma protein that binds retinol and thyroxine, transport vitamin A.
Curly hair: keratin disulfide bonds; sulfur in methionine and cysteine.
Collagen: ligament connects bone or cartilage (elastic, fibrous connective tissue converted to bone); tendon connects muscle with its bony attachment.
Hemoglobin heme(iron) and chlorophyll (magnesium) both have porphin ring.
Ribonuclease: a secreted enzyme that hydrolyzes RNA during digestion NMR align a magnetic nucleus (hydrogen atom) with external magnetic field, perturb this alignment using an electromagnetic field. NMR spectroscopy and magnetic resonance imaging.
Nucleotide is nucleoside monophosphate. AMP is a nucleotide.
CICADA recipe (drum-like membranes: tymbals)

Chap 06 A Tour of the Cell

Chapter 6: A Tour of the Cell

cells_prokaryotic Bacterial wall: peptidoglycan cell_sizes 1 m=1.09 yards; 1cm=.4 in. cell_differential-contrast POLARIZED GLASSES cell_brightfield cheek cell. cell_confocal Sections like CAT scan w X-rays. cell_em tracheal cell, sections thru cilia. surface_volume 06_07SurfaceVolumeRatio_L.jpg used in measure lab cells_animal Centrosome (upper left) contains 2 centrioles. nucleus Nuclear lamina made of protein filaments. ER Nuclear lamina made of protein filaments. RER: secreted proteins, membranes. SER: steroids. Glycogenin makes primer proglycogen -> glycogen synthase in Golgi. lysosome_phagocytosis Plant vacuoles may contain lysosome enzymes; macrophage ingest pathogens. microtubule Fibroblasts make collagens; heal wounds easy to culture. Centrosome contains a pair of centrioles. dynein Revu: dynein, cross-linking proteins. muscle Myofilament, head:

streaming Myosin motors interact with the actin. ===

Phase Contrast Microscope: light passing trough transparent part travels slower, increased to 1/2 wavelength by phase-plate.
Differential Interference Contrast: polarized beams detect difference in refractive index.
SEM: backscattered or secondary electrons, cover with conductive material.
Carbohydrate side chains of membrane glycoprotein (Glycosylation): cell-cell recognition, antigen-antibody; on outside of membrane (oxidizing env).
Extracellular matrix ECM: connective tissue in mammalian cells; structural proteins: collagen/elastin. Specialized proteins: fibrillin, fibronectin, laminin; Proteoglycans.
Junctions: desmosomes in skin, heart: subject to mechanical stress.
Tonoplast: membrane surrounds a vacuole.
Nuclear lamina: intermediate filaments made of lamin
nucleolus: ribosomal RNA synthesis and formation of ribosomes. Ribosome subunits: rRNA and proteins.
Smooth ER: lipds, steroids - sex hormones in gonads. Toxins (alcohol): liver, can build tolerance.
Peroxisome: enzymes transfer hydrogen to oxygen to detoxify alcohol, producing hydrogen peroxide (H₂O₂) & converted to wate; Photorespiration.
Camillo Golgi 1843.
Phagocytosis: Greek phagein = eat + cyte = Greek kytos = anything hollow + Greek osis = act or process
Plastids: chromoplasts yellow xantophyll and yellow/red carotinoids, leucoplasts store food molecules (amyloplasts or starch plastids in potato root).
Prokaryotic flagellum solid unit, primarily protein flagellin, rigid structure turned by rotatory motor like a propeller, much smaller than eukaryotic.
Microfilaments found in microvilli Sol-Gel fluid region sol, thicker region gel.
Cytoplasmic streaming: as membrane-bound organelles crawl along the inner cell wall they set the cytoplasm into motion. This streaming allows other organelles and nutrients to flow in the stream.
Middle lamella: outermost layer of plant cell wall; plasmodesmata pores through the wall. Secondary cell wall: sclerenchyma, collenchyma, xylem have lignified cellulose.
junctions: tight in epithelial (lung), gap in heart (ions -> action potential), desmosome (most common) in skin, strength & resilience. systole/diastole contract/relax
Motor proteins kinesins and dyneins.
In humans, basal body of sperm’s flagellum enters egg and becomes a centriole.
Myosin/actin: ATP hydrolysis to generate mechanical force

Chap 07 Membrane Structure and Function

Chapter 7: Membrane Structure and Function

fluid_mosaic Steroids can cross: hydrophobic. diffusion RAISIN/GRAPES/SALT - 2 cups/chopsticks. tonicity saline 0.91% NaCl, water_balance-animals DRINK FROM LAKE OR OCEAN? water_balance-plants TOILET PAPER: TURGID=swollen. endocytosis-receptor HHMI 7-12:30 Dengue Virus endocytosis; 2nd serotype 2nd binding not to lysosome. === ACT 7A: review labels in step 2 ACT 7F: step 2 answer always A

	1=b  2=c  3=a  4=D  5=B
	 6=c  7=b  8=b  9=A 10=c

Chap 08 An Introduction to Metabolism

Chapter 8: An Introduction to Metabolism

metabolism Anabolic-androgenic steroids protein synthesis "that which is thrown up, mound". cheetah Impala ewe? atp_hydrolysis coupled to catabolic reactions. sucrase Caramel=poly6saccharide. exergonic Free energy: can yield entropy to do work: the change (delta) is measurable. enzyme Hexokinase phosphorylates glucose -> glycolysis. enzyme_activity Trypsin produced in pancreas; 40°C = 104°F; body temp is 37°C. ===

		8eSQ: 1=b 2=C  3=b  4=a  5=e
	      6=c 7=C L → N

Chap 09 Cellular Respiration

Chapter 9: Cellular Respiration

NAD Two electrons and one proton (from food) in arrow at right. etc MENTION chemiosmosis. Cyanide inhibits cytochrome c oxidase. Pump protons into intermembrane space. anaerobic Probiotic: Lactic acid bacteria, yeasts and bacilli; colon cancer, cholesterol, blood pressure. ===

Chap 10 Photosynthesis

Chapter 10: Photosynthesis

autotrophs Purple sulfur bacteria: hydrogen sulfide -> sulfur. BBC-PlanetEarth/3.3_ShallowSeas/#29:00 Kelp forest preyed by sea urchins: urchin barrens. Solar sea slug plastid. absorption_spectrum Blu-ray DVD: violet laser (405 nm), rather than red (650 nm). chloroplast Cottonwood (Populus deltoides) leaves? overview 10&B: add 6H₂O to both sides of formula. Water released in Calbin (transpiration). excite CHLOROPHYLL solution: shine red light? Fluorescent mercury, neon (red) argon (blue), sodium. photo This is linear electron flow; P680 is a reaction-center chlorophyll a. chemiosmosis 10&D: stroma out; thylakoid space in. ETC in 2 places. c3 Water released in Calbin cycle (carbon fixation dehydration to 6-phosphoglycerate -> transpiration). ===

	8eSQ 1=c  2=d  3=a  4=skip Sutherland 5=C activation of G protein-coupled receptors.
	     6=B? 7=a  8=D?!?

Chap 11 Cell Communication

Chapter 11: Cell Communication

Viagra NO emission toxic -> nitric acid, react w ozone. Nitrous = N²O laughing gas, greenhouse. local_signaling Epidermal growth factor by submandibular gland, parotid gland, Salivary EGF. Para: beside, near. long-distance_signaling Exocrine: into ducts: tear salivary, mammary. ion_channels Facilitated diffusion diff: ligand and ions. G-protein Epinephrine as signal. phosphorylation_cascade Phosphatases off. nuclear Transcription factor mentioned in 11&E === 11&E Build Signaling Pathway - skip 2 iP3; 3 needs 3 (transcript factor); 4 needs 6 (protein kinase); 5 needs 3.

Chap 12 The Cell Cycle

Chapter 12: The Cell Cycle

cycle G1=primary growth, G2=microtubules. mitosis pro=before meta=after ana=back telo=tail. Metaphysics after Aristotle's Physics. Metabolism, Metamorphic. mitosis-anaphase Human cell has 92 chromosomes. mitosis-g2 Centrosome: 2 centrioles in animals; plants no centrioles. cytokinesisA Microfilaments=actin cytokinesisP Vesicles contain cell wall and membrane components. === ACT 12&C: non-kinetochore spindles lengthen in anaphase? two centromeres; kinetochore microtubules?

	8eSQ 1=b  2=a  3=1  4=C  5=C? MPF=degradation of cyclin
	     6=E=cleavage furrow formation?  actin=  7=a  8=b

Chap 13 Meiosis and Sexual Life Cycles

Chapter 13: Meiosis and Sexual Life Cycles

karyotype Light bands are GC-rich with genes; FISH: fluorescent in situ hybridization. ===

Chap 14 Mendel and the Gene Idea

Chapter 14: Mendel and the Gene Idea

pea WASABI PEAS; peanut embryo genes Define genome. segregation Separate in meiosis I, unless x-over. bloodABO Donated blood contains only RBC, no plasma. Type A has anti-B antobody, AB has none. Vid

melanin 8 possible F1 genotypes: AaBbCC missing? Eumelanin (red) and pheomelanin (brown). === Pedigree tutorial:

1=recessive(skip), 2=autosomal, 3=both parents, 4=recessive, sex-linked, dominant

	8e: 1=  2=d  3=A  4=b 5=b 6=D 7=c 8=D(C ok(?) 9=a 10=A

Chap 15 The Chromosomal Basis of Inheritance

Chapter 15: The Chromosomal Basis of Inheritance

drosophila-conclusion Sex: ratio between # of X and # of autosome sets, not just Y. XY Meiosis and sex determination: XX males and XY females Evolution of Y chromosome: adventures of crossing-over Evolution of human chromosome #2 (Ken Miller): why do humans have 46 chromosomes? haplo-diploid Copious protein-rich royal jelly to queen. Bumble colonial, carpenter solitary. X-inactivation Calico cat and X inactivation (random deactivation of an X chromosome) translocation_reciprocal Philadelphia proto-oncogene moves to short chromosome 22, escape cell cycle. ===

	8eSQ 1=e  2=E  3=a wild type  4=d unexpected  5=a
	     6=a  7=b husband irrelevant  8=c female werewolf must be heterozygous
	     skip mitochondrial
	A single mating can produce many offspring. 
	Drosophila chromosomes can be easily distinguishable under a light microscope. 4 pairs/2 weeks.

Chap 16 The Molecular Basis of Inheritance

Chapter 16: The Molecular Basis of Inheritance

xray 572.8092 FRA (Nichols) (VHS QH506 .S437 2003) 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 QH431 .D573 2002 Discovering DNA (IN LIBRARY USE) Watson/Crick: B form (wet), Franklin worked with Wilkins on A photo 51 ovarian 37; I94 2 mi S. of Gurnee Buckley Rd. double_helix lab DNA MODEL replication_fork Topoisomerase: break & rejoin backbone (PHONE CORD) Topoisomerase: the knotty problem of unwinding a double helix replication_bubbles Double helix 2 nm wide. elong Pol I fills gap & removes priner, II repair. leading ZIPPER fannypack: leading strand excision Nucleotide excision repair animation telomere Telomerase is Reverse Transcriptase. nucleosome A nucleosome has 8 histones w amino end (tail) out, separated by H1,. ===

	OK        3=b  4=c  5=b 
	6=d  7=a  8=c

Chap 17 From Gene to Protein

Chapter 17: From Gene to Protein

central_dogma 1970 Crick promoter Remove RNAP II. RNA_processing The 5' cap, 3' poly-A tail, and UnTranslated Regions facilitate ribosome attachment. triplets How many possible combos of triplets? 4³=64. genetic_code Asn=Asparagine, Asp=Aspartic Acid, Glu=Glutamic Acid, Gln=Glutamine mutation GAA -> GUA: bottom row, 3 and 1 mutation_nonsense AAG 3rd row, 3 mutation_missense AGC: 3rd row, 4 mutation_silent GGC -> GGU bottom. 4 === ACT17&B/3:

part 5 exercise: use red ribose;

ACT17&D/6:

translation: 45 kinds tRNA; use ATP to attach a.a. to tRNA, GTP on ribosome?

	1=C  2=B  C=D  4=E  5=B

Chap 18 Regulation of Gene Expression

Chapter 18: Regulation of Gene Expression

trp_regulation Central dogma: transcribed=expression lac_operon Ferment; beta galactosidase converts some lac to allo; cistron=locus -> polypeptide. lac_repressed lacI Inhibits by making repressor; operon also has lacY, lacA activator Distal control elements (far from promoter); note transcription factors. acetylation NSN_Epigenetics.mp4 3:00 mice agouti gene methylated (CH3) NOVA QH438.5 .G456 2006 Ghost in Your Genes: 13:00 Epigenetic deletion in chromosome 15, depends on parent. Epigenetic (ABOVE) change in gametes lead to genomic imprinting. splicing Troponin T muscle proteins - binds to tropomyosin to associate with actin. euk-regulation_cytoplasm Review 1:

says drgrade poly-A tail first. mRNA_degradation REVU; donot confuse miRNA w mRNA. cytoplasmic 2008 physics Nobel: spontaneous broken symmetry cytoplasmic_Drosophila 21 B Bicoid mRNA from nurse cells. determination MyoD (transcription factor) activates other genes, blocks cell cycle - multinucleate. proto-oncogene Transposable elements in ch21. ras is proto-oncogene; p53 tumor-suppressor. p53_tumor-suppressor Tumor-suppressor also repair DNA. Adenovirus and p53:

colorectal_cancer Colonoscopy === 8eSQ 1=d 2=a 3=d 4=a 5=c 6=e 7=a 8=c 9=b 10=b

Chap 19 Viruses

Chapter 19: Viruses

viral DNA used for replication AND transcription. virus Adenovirus bronchiolitis, ear infection. animal_virus VIRUS LOTTERY. Flu=RNA Orthomyxovirus HIV Note glycoproteins. Lyses T cells but not initial macrophages; killed by cytotoxic T. === 19&E: RNA-binding regulatory protein - NOT lac repressor that binds to operator (DNA); binds to 5? untranslated region (5? UTR) of mRNA, preventing ribosome attachment (UNUSED).

	1=C  2=A  3=A? 4=A  5=E  identical
	6=A? 7=C  8=C  9=B 10=B? ... division

Chap 20 Biotechnology

Chapter 20: Biotechnology

gene_cloning2 Tissue Plasminogen Activator (TPA) protein dissolves blood clots in heart attack. restriction Palindrome dates: 01/02/2010, 11/02/2011 cloning This uses hummingbird beta-globin gene, video human gene; beta-galactosidase digets X-gal. cDNA cDNA can be expressed in prokaryotic; shows which genes are expressed; reverse central dogma. PCR Primers can be DNA for Dideoxy; Thermus aquaticus: Taq polymerase HHMI 35:40 PCR 42 Sanger sequencing; 45-52 chip electrophoresis Anode is positive terminal fragment Dde I (one). fingerprint Short Tandem Repeats. The 3 DNA samples treated by Southern blotting w radioactive probes. termination Frederick Sanger also Nobel for sequencing insulin. transplantation QH442.2 .C743 2002: Creation#21:00 rat, 23:30 egg donor, Judson's skin cells thru zona pellucida (glycoprotein) - 32:30 QH442.2 .F67 2006: For spares or repairs. dolly Need to reverse epigenetic changes: acetylation of histones. ===

	1=B  2=B? 3=C  4=B  5=A? post-transcriptional processing
	6=C  7=E? 8=C? 9=D 10=C? DNA sequencing

Chap 21 Genomes and Their Evolution

Chapter 21: Genomes and Their Evolution

microarray NOVA-scienceNOW/Ep-2 (500 NOV Ep. 2) 2:20 GATTACA 4:30 SNP - 10:30 PSA test (76 MB, 20 min) Neil deGrasse Tyson astrophysicist, direct Hayden Planetarium genome_sequencing REMOVE this and also cloning and dideoxy from chap 20. Plasmid or phage vectors? Probably PCR. 6 billion bp=1k round trips to Sun. genome_comparisons Discovery-MiraclePlanet/5_SurvivalOfTheFittest/#39:00 (QE501 .B8182 2005) FOXP2 gene for speech ===

	Q  1=C  2=Ex 3=B  4=A  5=A? without cytokinesis.
	   6=D? 7=C? 8=A? 9=c? 10=E? master
	C  1=E  2=D  3=A? 4=D  5=D+
	   32=A? 33=A? 34=e? 35=A

Chap 22 Descent with Modification

Chapter 22: Descent with Modification

Beagle Galapagos 900 km (600 mi) W Ecuador; O of Species 1859 after essay from Alfred Wallace, 23 years. finches BBC-Galapagos/#14:30 Marine Iguana; 25:00 Tortoise 30:30 Hawk 35:15 Sea Lion fights Galapagos Islands video:

12 parts: boobies, iguana, tortoise. Tribulus SEEDS Puncturevine natural_selection Inductive reasoning (Jane Goodall chimpanzees). variation REPHRASE! overproduction PUFFBALL adaptation IMAX-SecretLife/#15:00 Flower Mantid (12:40 Arum and mosquito pollinator) HIV Reverse transcriptase in retrotransposons and telomerase. homology Whales 4 toes. Mammals diverged 65 MYA Practice activity (esp. whale)

embryonic Pharyngeal pouches - inner ear. convergent Southern flying squirrel in IL. transitional Order Artiodactyla 4 toes pigs, cattle, deer. Toothed whales: dolphins, Orca, Sperm Whale, Narwhal. Cecil Rhodes founded De Beers; Rhode Island, Rhodesia: Zambia & Zimbabwe. (Pakicetus, Dorudon nostrils); Anthracotheres cloven-hoofed even-toed ungulate. Baleen embryos had teeth, resorbed. Toothed whales: dolphins, Orca, Sperm, Narwhal. PBS-Evolution/2.2_change/#11:20 ->14:10 Basilosaurus (aquatic) had leg bones, Sinonyx wolf-like mammal 50 MYA. evolutionary_tree Amniotes -> Sauropsids (reptiles) -> Diapsida -> (flying or flightless Kiwi, not Penguin) ===

	8eSQ  1=b 2=c 3=D 4=dd 5=a 6=dx

Chap 23 The Evolution of Populations

Chapter 23: The Evolution of Populations

caribou Arctic National Wildlife Refuge. allele-variation Mummichog is a killifish; B, b alleles. hw Calculate genotype frequencies next (NOTE: this is incomplete dom). bottleneck BOTTLENECK REESE'S PIECES. bottleneck2 Studied 6 loci; bottleneck mid-20th C. Gene flow from other states -> egg hatch rate 90%. mutation Fused 2,4 etc: no allele change. Madeira: Atlantic/Portugal; mice intro 15 C, isolated by mountain. selection_intersexual Peacock Spider Female praying mantis eats male after mating selection_intrasexual BBC-LifeOfMammals/1.3_PlantPredators/#38:20 Bison, bighorn aheep, topi fight natural_selection NOVA-DarwinNeverKnew/#31:30 (576.82 WHA) Rock Pocket Mouse light/dark fur === Causes of Evolutionary Change:

only discuss 4 onditions; no nonrandom mating.

	8eSQ	1=D (70% is p; ask 2pq)  2=A  3=E  4=B(reshuffling of alleles=chief cause)  5=B

Chap 24 The Origin of Species

Chapter 24: The Origin of Species

cormorant BBC-Galapagos/#55:45 Flightless Cormorant species Western meadowlark: yellow throat touches cheek; biological species NA asexual/fossils. mule Hinny male horse, female donkey. prezygotic Gametic isolation in next figure! Bradybaena is diff from Euhadra snail. BBC-Galapagos/#2:08:50 Blue-footed Booby mating: foot-lifting, sky-pointing; 10:20 diving speciation-allopatric SW desert Ammospermophilus harrisii (Harris's antelope squirrel) SW AZ; A. leucurus (White-tailed Antelope Squirrel) CA. Kaibab darker body, separated 10K years ago, now subspecies. Mules on Kaibab and Bright Angel. speciation-sympatric HAWTHORNS. Apple grafting (align cambium layer) + pollen from compatible cultivar. autopolyploidy Anaphase is tetraploid. allopolyploidy REVU: Nondisjunction meiosis I; hybrid's chromosomes are not homologous. COTTON, tobacco cichlid Color -> territorial. Fusion discussed next. ===

	8eSQ 1=B 2=a 3=c 4=e 5=d 6=c

Chap 25 The History of Life on Earth

Chapter 25: The History of Life on Earth

strata BBC-Earth/Disc1/#28:50 (QE31 .S72 2007, 551 EAR Blu-ray) Stromatolites 29:50 Snowball Earth 1:14:20 Stromatolites photosynthetic 1:17:15 Banded iron Igneous, Metamorphic. Dimetrodon on LEFT: no scales, related to synapsid mammals. Plesiosaur not dinosaurs (terrestrial diapsid archosaur). Placoderm armoured fish Ammonite: Mollusca, Cephalopoda - octopus, nautilus. Geological Phanerozoic=.5 BYA. Archaen prokaryote; Proterozoic euk/multi. Ignore epochs. Fungi not shown? clock This clock actually 5 BY. H. sapiens 160KYA. Phanerozoic eon last 3 eras. Universe 14 B? oxygen Banded iron source of ore. endo Plastid: amyloplasts store starch. photosynthetic sea slug BBC-BluePlanet/3.6_CoralSeas/#5:30 Polyps 6:55 algae inside ("plants"=Dinoflagellata) 9:15 fight cambrian Taxa: Class Mammaalia, Order Primates -> Family Hominidae (apes). synapsids Descent from top skull. Cynodont=dog teeth. Why snake for reptiles? plates BBC-Earth/Disc1/#11:10 (QE31 .S72, 551 EAR Blu-ray) N American/Eurasian plates split 13:50 Pangea boundaries Fluid outer core (iron - magnetic), solid inner. drift This is Phanerozoic eon; Pangaea: Permian; breakup mid-Mesozoic. Gulf Stream warms Europe. extinctions Discovery-MiraclePlanet/4_ExtinctionRebirth/#5:00 (QE501 .B8182) Permian volcanic eruptions. Ordovician seems largest extinction? Tertiary=Paleogene + Neogene. KT Parasaurolophus, Megazostrodon! Asteroid belt Mars-Jupiter; meteorite: cold or warm climate? NOVA: Last Extinction (nanodiamonds in Greenland ice sheets: comet 13KYA killed ice age animals?) mammal_radiation Echidna: 4 species. radiation IMAX-HiddenHawaii/#9:40 Silversword Maui Haleakala 1,860 mi fr cont. 10-50 Y, 2m: agave yucca. ===

	REDO Permian, etc...
	8eSQ	1=c  2=a  3=E  4=B

Chap 26 Phylogeny and The Tree of Life

Chapter 26: Phylogeny and The Tree of Life

carnivora Badger, European Otter, coyote; gray wolf (dog Canis lupus familiaris). Canidae: Genus Vulpes are foxes. Phylogeny=genealogy. Homo_sapiens Class Mammalia, order Primates, Family Hominidae (apes). phylogeny Homology vs. analogy; same figure as clade; life Protista polyphyletic. ===

	SQ 1=B  2=D  3=B  4=E
	   5=d  6=c  7=d  8=a  9=e 10=c
	AQ 1=A  2=e  3=c  4=d  5=a  6=a  7=b
	   8=a  9=b 10=b 11=d 12=c 13=b 14=a 15=A
	CQ 1=c  2=B  3=d  4=c  5=D
	  21=a 22=E 23=b 24=c 25=e

Chap 27 Bacteria and Archaea

Chapter 27: Bacteria and Archaea

flashlight Flashlight fish Photoblepharon steinitzi. shapes S. throat; S thermophilus ferments lactate Swiss cheese (CO2 another bac). Spirochete: Lyme, syphilis. capsule protect from host defenses see transformation. Streptococcus pharyngitis spherical. endospore Layers protein coat. Discovery-MiraclePlanet/1_TheViolentPast/#29:00 Bacillus permians conjugation Donor has Fertility factor; can be diff species. transformation Streptococcus pneumoniae ear infection, pneumonia. ch16 Griffith 1928 did not know DNA; eukaryotes transfection: gene gun nanoparticle. gram negative: outer membrane lipopolysaccharide toxic and resistant. Diverse, paraphyletic. phylogeny G-positive at bottom. domains See top 2, bot. Streptomycin prevents ribosome binding formyl-methione in Bacteria! OwensLake Why named "Bacteriorhodopsin"? Photosynthetic proton pump -> ATP. Halophiles pump K⁺ ions in. Dry lake: water diverted for L.A. Harvest soda (Sodium carbonate). Trichodesmium (cyanobacteria) causes Red Sea, red tides. gram-positive Streptomycin binds ribosome treat TB. Mycoplasma small genome to study. Fibroblast -> collagen, wound healing. rhizobium Bacteroids in vesicles. lyme Exo spores can survive boiling: pressure processing. Endo: Salmonalla. Botulinum -> neuroplasticity. ===

	1=d  2=a  4=D? 7=C? 9=a
	1=c  2=d  3=b  5=e  6=a 24=d 27=c

Chap 28 Protists

Chapter 28: Protists

protista QR74.5 .B565 2004 The biology of protists (Circulation Desk) Ciliates has animation of cilia movement. eukarya Unikonta include Fungi, Animalia: single/no flagellum. plastid Chromoplasts make/store pigments; amyloplasts store starch. euglenozoa Not all green trypanosoma Tsetse biting flies feed on blood; can break b-b barrier. plasmodium Zygote -> meiosis. SOME gametocytes (n) reinfect RBC. Fever: merozoites released from RBC? dino Cellulose from photo hard to digest; carotenoids. dinos=whirling; deinos=terrible. ciliates REVU conjugation. amoebozoans Slime molds not fungi! cellular Aggregate amoebae like scifi/horror movie; 200 µm not quite visible. plasmodial Acellular (multinucleate)=diploid. See streaming in middle; maybe largest cell but G. algae Caulerpa. diatom Yellow, not green; oil for biofuel? seaweed BBC-BluePlanet/3.5_SeasonalSeas/#13:25 Kelp/bryozoans/Sea Otter feeds on shellfish BBC-PlanetEarth/3.3_ShallowSeas/#29:00 Kelp forest preyed by sea urchins, creating urchin barrens red_alga-Nori NORI. Agar (from agarose) is cell wall polysaccharide. Gelatin from collagen skin/bone. green_alga Supercell larger than plasmodial, snorkeling in intertidal. volvox Asexual not pregnant! Biflagellated like Chlamydomonas. === 28&A 3: photosynthetic clades: Euglenid + Dino + Diatom; 17: Cellular slime mold is multicellular

	1=d  6=d  8=a
	1=e  6=c  8=a 11=c 18=c 20=d 23=c 25=b

Chap 29 Plant Diversity I: How Plants Colonized Land

Chapter 29: Plant Diversity I: How Plants Colonized Land

eukaryotes Charophytes aquatic, sporopollenin protects zygote. charophyte Aquatic, sporopollenin protects zygote. alternation Difference from algae: embryo. embryo PEANUT EMBRYO. sporangia Sphagnum; spores always haploid. bryophytes MOSS SPOROPHYTE. sphagnum Put in /bryophytes.html, explain "leafy", retitle rhizoids REMOVE moss-cycle Exercise seta=sporophyte stalk. Capsule=sporangium, peristome disperses spores. fern-cycle Exercise mature gametophyte (herma) repeated bottom. Seed plants dioecious, sporophyll=mod leaf. pterophyta Horsetail abrasive Carboniferous Carboniferous before Permian. === WHY Bacteria and Archaea not 1 domain?

	8eSQ
	1=B shape?  2=E generations?  3=a  4=d  5=C?  6=b  7=C?
	8=b  9=a  10=a  11=b  12=a

Chap 30 Plant Diversity II: The Evolution of Seed Plants

Chapter 30: Plant Diversity II: The Evolution of Seed Plants

seed_plants Taxol also breast + lung. Quinine not used anymore. Gymno=naked (see Word Roots). Gymnosperm_cycle Exercise ovule top (scale=sporophyll) integument rite, sporophyll bottom; 2. CONES. Heterosporous. pollen_tube 2 eggs may be fertilized, but 1 survive. microspore DIAGRAM DOES NOT SHOW microspores. megaspore Megasporocyte -> 1/4 meiosis=megaspore. Ovule has 2 archegonia. flower Perfect=male + female. fruit PEANUT EMBRYO; BANANA 3, APPLE 5, ORANGE 10-13 carpels. Ovary wall=pericarp. Video: agouti buries seed. "www.commondreams.org/views03/0719-02.htm|Yes, We'll Have No Bananas|Common Dreams NewsCenter|7/19/03"! dispersal BURDOCK/MILKWEED/SAMARA. BBC-Life/9_Plants/ Candelabra Flower cartwheels like tumbleweed. Angiosperm_cycle Exercise anther top, megasporocyte bottom; 2. Germination: break dormancy. Angiosperm Grass no petals! Dicots: basal angiosperms (water lilies); magnoliids. ===

	8eSQ
	1=d  2=a  3=b  4=a  5=d
	8ePT (hard)
	1=e  2=c  3=a  4=D(hard)  5=a

Chap 31 Fungi

Chapter 31: Fungi

Armillaria "www.extremescience.com/biggestlivingthing.htm|Biggest living thing; Huge mushroom in Oregon|Extreme Science" fungus-structure Penny bun (Boletus edulis) mold Conidia=conidiophores? Penicillium is Ascomycete. Bread mold Rhizopus=Zygomycota. yeast Ascomycota; bud: unequal cytoplasm? life_cycle NO ALT of GEN (phytes no embryo). Zygote meiosis like plasmodium. REVU: germination from spores. Hyphae release pheromones mating types. Heterokaryotic: haploid nuclei. Exercise germination twice. 3 Zygomycota also germination twice. Zygomycetes_cycle Bread mold Rhizopus; heterokaryotic looks like zygote (egg). Pilobolus stalk swolls w sap explodes; light-sensitive. mycorrhiza 90% plants. Ascomycetes Asco + Basidio = Dikarya. Carp=fruit (chap 30 word root) Ascomycetes_cycle Dikaryo -> hyphae, not heterokaryo; conidia=asexual spores <- conidiophore. Tetrad. Basidiomycetes PUFFBALL, SHELF FUNGUS lichen LICHEN. leafCutterAnts Minim workers protect foragers from parasitic flies. BBC-LifeOnEarth/1.4_TheSwarmingHordes/#44:10 Parasol (Leaf Cutter) Ants ===

	8eSQ
	1=b  2=C  3=d  4=e  5=b  6=a
	8ePT (Not good)
	1=d(chemo) 2=b(plants) 3=d  4=c  5=b(coenocytic)
	30=e athlete's foot/yeast infections

Chap 32 An Introduction to Animal Diversity

Chapter 32: An Introduction to Animal Diversity

Cambrian Phanerozoic eon. Seascape: Wiwaxia and Sanctacaris. "paleobiology.si.edu/burgess/index.html|Strange Creatures - A Burgess Shale Fossil Sampler|National Museum of Natural History" body_plan Ctenophora=comb jelly. Some flatworms (Planaria) are acoela. triploblastic Archenteron surrounded by endoderm; coelom by mesoderm. Tube: mouth + anus. Left is protostome. coelom Pneumatic air-filled tires absorb shock. Mesoderm 2 layers. acoelomate Planarians are acoelomates; most Platyhelminthes are Lophotrochozoa. protostome Spiral: small cells in between larger cells at 8-cell stage: edges overlap. deuterostome Coelom <- folding of archenteron (endo). Ecdysozoa BBC-LifeInTheUndergrowth/1.2_TakingToTheAir/#42:50 17-year Cicada (play TakingToTheAir) === 32&A: Namatoda & Arthropoda are Ecdysozoa; #4 bilateral includes echinoderms. #5 diplo cnidaria. #6 triplo same as #7coelom. #7 coelome includes Nematodes. #8 Nematodes not coelom (psuedo).

	1=a  b=c  d=c  4=e  5=b  6=c  7=b  8=e  9=e 10=d
	1=b  2=b  3=b 24=c
	1,2=Porifera  3=cnidaria  4,6=E, etc  5=cnidaria  7,8=E,XNematoda?  9=Nem  10=Mollusca,etc  11=E,C  12=

Chap 33 Invertebrates

Chapter 33: Invertebrates

Annelid BBC-BluePlanet/3.6_CoralSeas/#3:30 Christmas Tree Worm sponge Spicules w spongin protein; cellulose; Luffa fruit. PBS-ShapeOfLife/1.1_Origins/#29:00 feeding. phylum_Cnidaria BBC-BluePlanet/3.6_CoralSeas/#9:15 Coral polyps fight, 13:25 Humphead Parrotfish cnidaria BBC-BluePlanet/3.6_CoralSeas/#40:00 Coral spawning hydrozoa Obelia fluke Swimmer's itch: birs are primary hosts. trichinella Muscule pain, breathing, heart failure. cephalopod BALLOONS jet propulsion. Blue blood: copper-rich hemocyanin, 3 hearts. gastropod BBC-BluePlanet/3.5_SeasonalSeas/#5:55 Jellyfish polyps 23:55 Sea Slug Navanax stalks Janulus mollusca Many scrape food using rasplike radula with backward-curved "teeth": ciliated larva: trochophore leech CUE UP NSN_Leeches.mp4 6:00-9:00 severed fingers, hirudin blood thinner myriapoda Sub-phylum. arachnid Also Demodex mites in hair follicles. arthropoda First 3 pairs legs end in pincers. echinoidea Sand dollar. echinoderm Mouth at bottom. WVS locomotion, gas exchange. ophiuroidea Brittle crawl. PBS-ShapeOfLife/3.6_SurvivalGame/#18:00 Sunf. starfish >abalone: scallop eyes. ===

	8eSQ
	1=C Cnidaria and Bilateria!  2=a  3=d  4=E exoskeleton?  5=B locomotion, gas exchange  6=e

Chap 34 Vertebrates

Chapter 34: Vertebrates

nerve Flatworms also have nerve cords. pharyngeal slits - inner ear. notochord Nerve cord not shown, next diagram shows spinal cord. craniate Cranium not in invert. heads! Neural tube -> CNS (nerve cord?) chondrichthyes Cartilage chondrocytes -> collagen; between bones, rib cage, ear, nose. Paired fins -> tetrapods? osteichthyes BBC-BluePlanet/3.5_SeasonalSeas/#32:40 herring bait ball hunted to last OR 44:20 lungfish But swim bladders may have evolved from lungs? lobe-finned Flattened head like croc. PBS-Evolution/2.2_change/#22:50 Acanthostega forelimb with fingers tetrapods Devonian-Carboniferous 300-400 MYA amphibia Poison arrow frog. amniotes Turtles anapsids? Parareptiles early, extinct; 2 Tuatara species NZ islands extirpated by rats. amniotic allantois also exchanges gases. birds BBC-Galapagos/#40:20 Waved Albatross mating ritual CHICKEN furcula=fused clavicles. Ratite: Ostrich, Kiwi, S. American rheas. snake Males use spurs for courtship and fighting. turtle Vertebrae and ribs fused to the carapace; shoulders within ribcage. mammalia Expand this. monotreme Short-beaked echidna. marsupial BBC-LifeOfMammals/1.1_AWinningDesign/#7:25 Echidna 11:00 Platypus 21:00 Kangaroo joey monkeys NW: squirrel monkey, capuchin. OW: mandrill, baboon, rhesus. bipedal Not truly bipedal like drawing! art NSN_SeaLions.mp4 2:00 sound, 3:00 "open", 4:30 tests (operant) NOVA Ochre=earth pigment: iron oxide; Blombos Cave. homo_habilis Brain 700-900cc, vs. 400 Australopithecus; 1200 human; rudolfensis contemporary w habilis. ===


Bio1151 notes	Updated: Dec 10, 2011.	Peter Chen