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by: Kimberlynn Seifert


Marketplace > Pennsylvania State University > Biology > BIOL 110 > CUMULATIVE NOTES for COURSE
Kimberlynn Seifert
Penn State
Biology: Basic Concepts and Biodiversity

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Notes/Study Guide Used for BIOL 110. Earned an A in the class last semester. Notes include everything covered in the tutorials for BIOL 110 except the basic concepts for Punnet Squares. Using th...
Biology: Basic Concepts and Biodiversity
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This 51 page Bundle was uploaded by Kimberlynn Seifert on Saturday May 9, 2015. The Bundle belongs to BIOL 110 at Pennsylvania State University taught by Vasey in Fall 2015. Since its upload, it has received 117 views. For similar materials see Biology: Basic Concepts and Biodiversity in Biology at Pennsylvania State University.

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Date Created: 05/09/15
Biology 110 Study Guide Final EXAM 1 Tutorials 16 Tutorial 2 Properties of Water and Macromolecules Water 0 Water is a polar molecule 0 Hydrogen bonds hold water together creates cohesion High speci c heat 4 Main Classes of BioMacromolecules Carbohydrates Proteins Nucleic acids Lipids Carbohydrates Carbon oxygen hydrogen 0 Formula CnH20n Monosaccharaides are monomers of carbohydrates Gucose fructose Disaccharides are two monosaccharaides Sucrose lactose maltose Formed via dehydration synthesis loss of water molecule to link Polysaccharides Gycogen chitin starches cellulose Energy storage Structura Proteins Amino acids monomers of proteins Rgroups form Hbonds with neighbors leads to protein folding General structure of Arnin Acids l Garbdtryl a group Amino Group Structures of Proteins aria E mun Amino acids Primary Protein structure sequence of a chain of animo acids Pleated sheet Alpha helix Secondary Protein structure hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern Pleated sheet Tertiary protein structure threedimensional folding pattern of a protein due to side chain interactions Alpha helix Quaternary protein structure protein consisting of more than one amino acid chain Lipids Carbon and hydrogen equally electronegative Nonpolar makes the molecule hydrophobic Generally single molecules 0 Saturated Lipid each carbon bonded to the maximum amount of hydrogen Unsaturated Lipid has double bonds between carbons Phospholipids amphipatic hydrophilic and hydrophobic forms phospholipid bilayers cell membranes Steriods sex hormones are lipids pass easily through cell membranes hydrophobic allows rapid action of hormones Nucleid Acids DNA and RNA Monomers nucleotides Nucleic acid polymer Tutorial 3 Antiquity of Life 0 Earth is approximately 45 billion years old 0 First evidence of organisms 35 billion years Uniformitariansim assumption that the same natural laws and processes that operate in the universe NOW have always operated in the universe in the past and apply equally everywhere Early Atmosphere of Earth 0 Water vapor 60 highy Carbon Dioxide 25 Sulfur and sulfur compounds lll Dating Fossils 0 Relative dating deeper sedimentary layers formed earlier and their fossils are older than those found in shallow layers ofrock Absolute dating radiometric dating dendrochronology Tutorial 4 Prokaryotes I Cellular and Genetic Organization Prokaryote Morphology simple singlecelled Cocci round Bacillus rodshaped Spirillum helicalspiral Features of Prokaryotic Cells Smaller than eukaryotic cells 0 Lack membrane bound nucleus 0 Lack organelles DNA is circular not linear Have Cell walls Archaea vs Eubacteria Archaea Eubacteria Lack peptidoglycan in cell 0 Have peptidoglycan in cell walls walls 0 Different membrane lipids Normal membrane lipids Genetic organization more 0 Lack introns and histones similar to eukaryotes in DNA 0 Gene expression closer to 0 Some are photosynthetic eukaryotes Some are pathogenic None are pathogenic lncludes extremophiles Prokaryotes Reproduce Asexually Binary ssion dividing in half produces two genetically idenUcalceHs Cell division in as little as 20 minutes 0 Rapid cell division rapid evolution Genetic variation Mutations in DNA replication isn t perfect 0 Horizontal Gene Transfer transformation pick up DNA from environment transduction need a virus bacteriophage conjugation need a bacterial partner two join together Plasmids vs Chromosomes Plasmids DNA replicates independently from the chromosome Chromosomes carry genes that are essential to survival Tutorial 5 Prokaryotes ll Structure and Function Gram stain used to differentiate bacteria based upon amount of peptidoglycan Gram bacteria a lot of peptidoglycan less complex cell wall Gram bacteria less peptidoglycan complex cell wall contain lipopolysaccharides some are toxic defense against host cells resistant to antibiotics Movement of Prokaryotes Many capable of directional movement Flagellum long appendage specialized for locomotion Taxis orientated movement toward or away from stimulus 4 Primary Metabolic Modes 1St part of the term where the organism gets the energy to make ATP Photo use light energy to make ATP Chemo use break down of carbon molecules to make ATP 2nOI Part of the term where the organism obtains its carbon Autotroph can x carbon from gas C02 into solid form Heterotroph can only obtain carbon from other solid carbon molecules gt39ltphotohetertophs and chemoautrophs are seen only in prokaryotes Tutorial 6 Prokaryotes Ill Evolution and Early Metabolism Symbiosis An extended and close association between two species Mutualism bene cial to both species ie nitrogen xing bacteria with plants Commensal bene cial to one species neutral to the other ie movement of cattle stirs up insects in grass for food PaLsitic bene cial to one species harmful to the other ie salmonella tapeworms Exam 2 Tutorials 713 Tutorial 7 Subcellular Architecture of Eukaryotic Cells 0 Cells remain small to maximize their surface are to volume ratio 0 Need high ef ency to maximize surface area gt39ltgt39ltcytoskeleton at end of fungi information Organelles specialized structures that are separate from the rest of cell by a phospholipid bilayer Nucleus most viable organelle provides genetic information surrounded by a double membrane called nuclear enevelope Nucleolus contains a very active group of genes that encode and transcribe ribosomal RNA Ribosomes produce proteins Golgi Modi es sorts packages proteins Lysomes disposal of waste digestion hydrolytic enzymes Mitochondira provide energy own circular DNA Endomembrane System 0 Modi cations take place in a network of membranebound chambers called endomembrane system Begins in endoplasmic reticulum Smooth ER lipid synthesis and metabolism carbohydrate synthesis degrade toxins Rough ER houses ribosomes on surface protein assembly Tutorials 89 Protists Endosymbiont Theory mitochondria and chloroplast were bacteria mutualism in host cell membranes similar to prokaryotic membranes circular DNA own protein synthesizing machinery binary shion Protists Eukaryotic Mostly Unicellular Convergent evolution process by which unrelated organisms that occupy similar enviroments evolve similar traits Any eukaryote that is not plant animal fungus Paraphyletic Kingdom Alveolata Monophyletic Alveolae cavities in membrane Dino agellates Ciliates Apicomplexans Unicellular Aquatic Cellulose armor Perpendicular agella 0 Both photo and hetero troph Can be bioluminesce Algal blooms ie zooxanethellae mutal with coral reefs cilia nt ism Monophyletic Move using 2 nuclei parasitic apical complex microtubules that puncture hostceH ie malaria Kingdom Stramenopila hair like projections on agella use chlophylls a and c Diatoms Bacillariophyta Oomycetes Brown Algae phaephyta most abundant photsyntheic organism x 20 of C02 lamentous growth like hyphae waterdowny largest protest multicellular consists of blades stipes holdfast molds similar to fungi ie potatoe nblight fruit blights silica cell wall abrasive many uses ie kelp many uses food thickener ice cream medicinal Kingdom Rhodophyta Red Algae phycoblin red color pigment use blue and green wave lengths allows plant live in deeper sea multicellular seaweed used as seaweed in sushi carageenan Kingdom Chlorophyta Green Algae most similar to plants contains chlorophylls a and b stores food as starch alternate generations as haploid and diploid Modi ed Mitochondria Parabaslids Kinetoplastids Euglenoids Diplomonads pathogenic two 0 lack golgi one large agella parasitic mitochondir engulf always have a prey via agella kinetoplast phagOCy heterotrophic organelle tOSiS stores extra have ageHa have golgi DNA i i Slime Molds kingdom amoebozoa similar to fungi Plasmodial Cellular individual cells fuse to form one large cell with multiple nuclei mostly single fuse together when resources are short retain cell walls Tutorial 10 The Cell Cycle Mitosis Cytokinesis Mitosis Process by which eukaryotic cells divide DNA replicates BEFORE cell division in S Phase Produces two daughter cells with same ploidy as the parent cell same number of chromosomes Used by Single celled organisms for Reproduction Used by Multicellular organisms for Growth Chromosomes Chromosome one molecule of DNA compacted with proteins Different chromosomes encode different genes Sister Chromatids Duplicated DNA from one chromosome Centromere the area where sister chromatids are attached to one another Condensed Chromosome a chromosome which has coiled itself into a super compact visible unit w one Chromosome unduplicated one Chromatid its sister chromatid one Chromosome duplicated G DIF INTEHPHAEE F lP iHlASE P HDMETAIPHASE Eentmenmee Ghmmatin Earlyr witmil Aster Fragamenz le itinetehere with eetriale pair39s dupmmatgd epille emmmem er nuzlelear mnnkm m hn 39 7 ENE399 I miemtubule a l39 39 4 r 7 I V n 1 r 1 a ii i 39 v i quotl l Kineteehere lNiueleelue Muralear Plasma Ehrer neemneieeneieting envelope membrane of two eieter ehromatide mieretubull39 Tl39ll39l ETAF39HAElE AlNlAPH EE TELD PHASE AME EWDKINESIIS Maeiaphase cleavage Mueleolue mate furn w v 39 f il llgl Nuclear entrnenme at Daughter enuelepe spindle Ell39zIE spindle pole ehrnnrineeumee firming Cytokinesis cell separation Animal cells contractile ring of actin micro laments cleavage furrow 0 Plants grow growth plate in middle because of hard cell wall Tutorial 11 Meiosis 0 Sex does not require reproduction 0 Sex recomnination of genetic information Chromosomes Genes and Alleles Genes sequences of DNA that code for a protein Alleles variations in the DNA sequence for that gene Result in variations in the protein produced Chromosomes One long piece of DNA that contains several genes Gene location on a chromosome is called a locus or loci plural Two Ways for Genetic Variation 1 Crossover of homologous chromosomes during Prophase l Exchange of DNA creates unique chromosomes 2 Independent Assortment in Metaphase l Large number of possible chromosome combinations means large number of genetically unique gametes mowiow of tiloiooio duplication f Ehmmosomes quot Moneoiolt or Cll39il mma ds Homologous Fair of Ehromooomeo thrownamids Ill ooloio Gomotoo Possible Chromosome Arangements of possible arrangements n of pairs Tutorials 12 and 13 Fungi Fungi Kingdom 0 Most closely reated to animals Multicellular except for yeasts m Spores that pmduce axesuaHy Chemoheterotrophs 39 Absorpitive nutrition Aqrnqnnrpq qnnrpq nrndlirpd Cell walls made up of chitin Store food as glycogen hyphae thin laments maximizes surface area septa internal walls that divid hyphae Fungal Life Cycle Haploid most of life 0 Sexual reproduction not necessary triggered by environmental stress Plasmogamy fusion of cyctoplasm from two hyphae remain in heterokaryotic stage for extrended period of time Karyogame fusion of haploid nuclei to form diploid zygote l Key l Haploid n Heterokaryotic unfused nuclei from different parents Diiploid 2n Spores o a SEXUAL 0 o ASEXUAL x REPRODUCTION REPRODUCTION 39 r 39 liE lEl iil iillliliiljliit illiiillll 0 o 0 Spores Important Symbioses with Fungi Lichens Mycorrhizae Chytridiomycota Microsporidians Can live in 0 Root fungi Aquatic fungus All are harsh Mutalisitc lnfects skins of intracellular enviroments relations amphibians parasites of 0 Break down whip with Massive protists and minerals plants population animals Used to 0 Plants declines Currently monitor air provide 0 Extinction of working to pollutions carbon some frogs develop Mycelium something increase that decudes surface area malaria to absorb water and nutrients Lives inside or outside the plant Zygomycota Predominately terrestrial sapbrobes Mostly bread and fruit molds Glomeromycota Intracellular mycorrizae Form structure called arbuscle Arbuscles aid nutrient transfer between fungus and plant Arbusculaar mycorrhizae in 80 of plants Basidiomycota Gilled fungi 25000 known species edible mushrooms after meiosis spores hang from tip of basida cells nuclei fuse only in cells at the tips of hyphae called basidia Ascomycota Sac Fungi 75 of known fungi ascussac sexual reproductive structure includes yeast truf es Yeasts Bananas l Ants singlecelled fungi I1aturaHy occuron skhwof fruitshuman s 0 many uses intestines of animals Soil fungus All are 0 Killed 6 Extremely parasites million bats hard to Alters Wakes bats eliminate behavior of from Reduces hosts hibernation production Mycelium Disease by 50 replaces comes from tissues Europe Arthopds and insects go crazy Cytoskeleton Micro laments Intermediate Fibers Microtubles Smallest bers 0 Made of protein actin Faciiate ceuar migration ie muscle contraction Fibrous proteins wrapped around another Anchors organelles Static in cell Largest Hollow tubes made of rows of paired tublim molecules 0 Major strucutural role 0 Important to cellular events mitosis Exam 3 1421 Tutorials 1416 Animal Diversity De ning Features of Animals Multicellular Eukaryotes No cell Walls lngestive Heterotrophs Food digested internally Tissues Range from none minimal to complex Nervous System Except Sponges Muscles Except Dipoblasts Mobile at some point in development or life cycle Tissues Collections of cells specialized to perform particular functions within an organism Eumetazoans have true tissues Parazoans do not have tissues Sponges are the only animals that lack true Ussues Embryonic Layers Animals with 2 layers dipoblastic Endoderm and Ectoderm Animals with 3 layers tripoblastic Endoderm Ectoderm and Mesoderm Development of zygote produces layers of cells that develop into different types of tissue Digestive tissue and internal organs endoderm Skin and nervous tissue ectoderm Muscles connective tissues circulatory system mesoderm Animal Development Cleavage Cleavagevery early embryonic cell divisions Indeterminate cleavage the cell can develop into any cell Humans Determinate Cleavage the cell can only develop into one certain thing Blastula I hollow sphere Eleavage Fertilized nf rnllc Egg Eygote Blastocoel the empty space inside the Archenteron space formed by gastrulation Develops into the digestive tract Eros sec Gastrulation surface cells move into blastocoel Differentiates into quot 11 Endode rrn EctodErrn Hoxy Genes and Body Segmentation Hox genes clusters of master control genes Control body formation patterning in embryonic develop of all animals gt39ltOver 95 of animals are invertebrate Sponges phylum Porifera Parazoa Sponges are sessile animals with NO true tissuesll 1St bifurcation in tree Lack Symmetry asymmetrical Minimal cell differentiation No Hox genes Filter feeders Cnidarians phylum Cnidaria Eumetazoa Radial Symmetry Dipoblastic Two Tissue Layers Endoderm Ectoderms Includes Jelly sh Corals Hydras Sea Anemones Sea Pens Carnivores Tentacles capture prey and move to mouth Tentacles have stinging cells called Cnidocysts Nematocysts Stinging organelle in cnidocysts Bilateria Three tissue layers therefore true muscles 0 Body cavity does not mean digestive tractgut all animals have a gut leeeelem ete Benjy ee uering quot Efrem eetedennj Tieeue lletl regien lirem meeederm Diekeetivetreet I 39 quot Flailwe r39r n V lrem endedennl Ceelemeie Eeely eevenng frem eetederrn Tieeue lleel regien 39 39 I A fre39m meeedermi a ggggggggggggggggggg Digestive ireei 39 39 frem endederm 39 39 Ceelem 39 V Eiedgr watering H H v v T39 lfrern eetederrnj u v TieeueJ39I39iliee egien r Efrem meeeclerm Digeetive freer r frem endederm c Peeudeeeelem Flatworms Cephalization Digestive tract has only one opening mouth anus Free living parasitic Nematodes Psuedocoelomates Complete digestive tract o Anus Coelomates True Body Cavity Coelomates classi ed based on early development Protosomes mouth develops rst spiral determinate cleavage Deuterostomes anus develops rst radial indeterminate cleavage Protosomes Deuterostomes LUHLHTII ll C Ell l l rth enteron A a frmatin quotI I i i i i 3 i u i u H 4 i r J r L 1H 3 V 39 1 1 magg l Celern I L LL L L E i Macadam r r Email lastier Ella Ef l DI E r whi m alm quotall anl39nrnr39nElnl mil Mollusks phylum Mollusca Gastropods Bivalves and Cephalopods Soft bodies usually a shell Similar body plan diverse appearances Mollusca Gastropods Largest group of mollusks 80 include snails and slugs Fresh water salt water and terrestrial Only group with terrestrial species Terrestrial gastropods use mantle cavity as a lung Most have single spiral shell Sea shells are from marine gastropods Slugs have lost shell and mantle use gills for breathing Mollusca Bivalves Marine and freshwater includes clams oysters mussels and scaHops Shells that are divided in two halves hinged by strong muscles Most are sedentary suspension feeders Bury themselves in sea floor or attach to a substrate Mollusca Cephalopods Includes squid octopi cuttle sh and nautiluses Fast agile predators Large brains and sophisticated sensory organs including complex eyes Shells Nautilus has external shell Squid amp Cuttle sh reduced internal shell Octopus No shell Arthropods phylum Arthropoda Segmented animals with jointed appendages and a chitinous exoskeleton These 3 features are the source of diversity and success in this group Over 1 million species lncludes lobsters crabs barnacles spiders and insects Typically have a head thorax and abdomen Joints in appendages allow them to bend Phylum Arthropoda Chelicerates lncludes spiders scorpions ticks mites and horseshoe crabs Most in class Arachnida Most are terrestrial Have clawlike feeding appendages called chelicerae Only have two body segments Phylum Arthropoda Myriapoda centipedes and millipedes Terrestrial Long body with numerous unspecialized segments Millipedes herbivores with two pairs of short legs per segment Centipedes carnivores with one pair of legs per segment Phylum Arthropoda Crustaceans Crustaceans Crabs lobsters shrimp barnacles Almost all living species are aquatic Two pairs of antennae Mandibles mouthparts that can be used for biting and chewing Appendages with 2 branches Phylum Arthropoda Hexapoda Includes insects Body plan head thorax abdomen three pairs of legs two pairs of wings some exceptions Complex life cycle most include metamorphosis from distinct larval form to adult Deuterostomes Echinoderms and Chordates Echinoderms Larvae with bilateral symmetry Aquatic Spiny skin Endoskeleton Water vascular system tube feet 0 Five part symmetry as adults 0 Sea Stars Sea Urchins Sea Cucumbers Brittle Stars Feather Stars Phylum Chordata Contains invertebrates and vertebrates 3 subphyla 0 Two comprised of invertebrate organisms Urochordata and Cephalochordata Subphyla Vertebrata contains all vertebrate organisms Four de ning features of chordates exhibited at some point during development or life cycle Notochord lies below nerve cord provides support develops in invertebral discs in vertebrates Dorsal nerve cord develops into brain and spinal cord Pharyngeal slits openings in throat pharynx Postanal tail Chordata Subphylum Vertebrata Pronounced cephalization Distinct head housing primary sensory organs and brain Cranium Protective casing for the brain Vertebral column Forms axial endoskeleton skull ribs spine Protects dorsal nerve cord Support head cranium brain Protects organs Anchor muscles Vertebrata law Evolution Jawed sh have paired ns and tail Maneuver in water quickly and effectively Enhanced predation esp when coupled with jaws Three main lineages Chondricthyans cartilaginous sh sharks and rays Ray nned sh tuna trout gold sh seahorse Lobe nned sh coelocanths and lung sh Challenges for Early Tetrapods Gas exchange Breathing air vs using gills Water conservation Dessication Structural support Bear weight on land Locomotion Adapting sensory organs for air and being on land Reproduction Amphibians First tetrapods able to move on land Includes salamanders and frogs Use moist skin to supplement lungs for gas exchange Still obtaining oxygen from water Return to water to reproduce No way to prevent gametes and eggs from drying out Undergo metamorphosis from larval stage to adult Evolution of Amniotic Egg Allowed early reptiles to move away from water and colonize completely dry land Allowed reproduction on land Embryo protected from dessication Eggs could be laid away from water lnternal fertilization Prevent sperm from drying out Production of fewer eggs per clutch Reduced predation of eggs Loss of larval stage Develop into miniaturized form of adult in egg Reptiles birds and mammals are amniotes Features of the Amniotic Egg Egg has 4 internal membranes Amnion uid lled sac surrounding embryo Yolk sac store of nutrients for developing embryo Allantois helps dispose of metabolic wastes Chorion and allantois obtain 02 from air and release C02 Reptiles Includes lizards snakes turtles crocodilians and dinosaurs Skin covered with scales waterproofed with keratin Obtain most of their oxygen using lungs Ectothermic coldblooded Birds Evolved from twolegged dinosaurs theropods Highly adapted for ight Reduced body weight Lack teeth Reduced vertebrae in tail size and number Feathers with hollow shafts Honeycombed bones Ectothermic warmblooded High metabolism Mammals Endothermic amniotes with Hair insulates body Mammary glands produce milk to feed young Three main lineages based on anatomy and reproduction Monotremes Marsupials Eutherians placental Mammals Monotremes Egg laying mammals Have both reptilelike and mammallike traits Only living species are Echidnas Duckbilled platypus Lack nipples Milk secreted from glands in skin Mammals Marsupials Include kangaroos opossums wallabies wombats and koalas Embryos develop internally in a placenta modi ed amniotic egg Brief gestation Give birth to underdeveloped young that complete development in abdominal pouch Young nurse from nipples inside pouch Mammals Eutherians Bear fully developed live young Often called placental mammals because have a more complextrue placenta than marsupials Over 50 of species are rodents or bats Exhibit wide diversity of Behavior Limbs Teeth Such specializations have allowed some eutherians unlike other mammals to Become aquatic Fly Live in social groups Become very large r I V a l y 39 39 L Mammahia Mammals E g m 1 E Reptiiha 39ulE ames Eiiraja hmphihia E mpnmaangj man Ha ir MESGEE id Damimm a E y h We Emmanmmwa Emma Em raysi m l tiq Egg gnatha L395 magiraga ak35 Ee hal c rda a Lanmlata szag d 39i39eeth ami Um mr ma T r lfiZEIEi Gawawrag I Wienebrae Ratlifera mtil ars l i n aatrall Emma L Tam e eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee ee Namatda mundwrms LLuEpDEELU lm a I 4 1 llaja l dWEIQLJll 2 w J I1 22 3 M II quotEHE EII en smu arm ZI39JEEEJEIWIdll l imamuw g Ejea gnagy Mr lllluska flag nu UtIi39IUIE Emailing l SEW 1m mm mm Air hmpuda Bags E155 3E1 ifquot E1 5 H a T i C Elm m 11 GE 9397 g Tutorial 17 Energy I Thermodynamics Thermodynamics Study of energy transformation First Law of Thermodynamics energy can not be created or destroyed it can only change form Amount of energy in the universe is constant Plants DO NOT MAKE ENERGY Second Law of Thermodynamics entroypy of the universe is always increasing Most disorderd form of energy heat Energy is Obtained from food Forming bonds releases energy The amount of energy depends on the atoms and the molecule Smaller molecules more stable Forming bonds releases a lot of energy Large molecules less stable Forming bonds releases little energy Catabolism goes from large unstable molecules to small stable molecules Bonds in unstable molecules require small amounts of energy to break weak bonds Bonds in stable molecules require large amounts of energy to break strong bonds Bond formation in small stable molecules releases large amounts energy More energy is released than used when small molecules are reformed from large molecules pmduct Energy quot 1ergy i i rleaeedf lll I I a 5 Free Energy 2 energy I N J not Energy released Energy supplied tQUIIIDl Ium when AG approaches zero NEGATIVE AG exergonic reaction releases energy Spontaneous reaction POSTIVE AG endergonic reaction requiresabsorbs energy Nonspontaneous reaction Reactions with negative D6 are spontaneous energy is released Reactions with positive D6 are nonspontaneous energy required Activation Energy For bonds to break energy input is required Activation Energy can be too high to obtain May require Enzymes Coupling Reactions release of exergonic reaction supplies energy required for endergonic reaction Enzymes Enzymes specialized subset of proteins that catalyze reactions Catalysts increase the speed of reactions without being changed in the process Shape of enzyme must match shape of substrate Lockandkey t high speci city Substrates bind enzyme at active site ATP Reduce activation energy Molecule that fuels most work within a cell Breaking and reforming bonds release energy Can move from sites of food catabolism mitochondria to where energy is needed Energy released from food catabolism is used to make ATP Hydrolysis of ATP releases energy to power anabolism The bonds in ATP are highly unstable Tutorial 18 Energy ll Cellular Respiration Glycolysis and Fermentation Cellular Respiration Converts the chemical energy in glucose to the more usable molecule of ATP Each glucose results in the production of 29 ATP max Comprised of 3 distinct processes Glycolysis Kreb s Cycle and the Electron Transport Chain Electron Carriers Electron carriers shuttle electrons Function is to harness electrons lost from oxidation during steps of cellular respiration Similar to how ce uses ATP for short term energy storage Shuttle electrons to the Electron Transport Chain edgeff39f r goes to pick a gagged R up more electrons NAD NAD H A I f elgflarpiration reduced L I used inflater F 1 NAD is reduced by one 2 NADH is the 3 NADH releases Hydrogen atom FEdUCGd TOFm It two e39 to the and one electron 0W cames tWO electron transport from a second extra GleCtmnS chain and another Hydrogen atom and releiief one J proton H Glycolysis m 2 ADP Occurs in ALL cells 2 NAD Occurs in cytoplasm 2 ATP Does not require oxygen 2 NADH 2 ADP InpUt 2 2H 2 Output 4 ATP 2 NADH Net Gain 2 ATP 2 NADH Fermentation In aerobic conditions 0 present Pyruvate and NADH move into mitochondria to be used in the Kreb s cycle and ETC respectively NADH is converted back to NAD by releasing electrons that are transferred to 02 at the end of the ETC Oxygen is the terminal electron acceptor In anerobic conditions 02 absent There is w 02 to take electrons to allow conversion of NADH back to NAD Without NAD gycoysis cannot continue Fermentation is used as an alternate pathway to convert NADH to NAD Lactic Acid Fermentation Used by animals as well as some bacteria and fungi During intense exercise if muscle cells can t get enough 02 they use fermentation Lactic Acid is also used in yogurts soy sauce and some cheeses Ethanol Fermentation Used by yeast fungus and some bacteria Produces ethanol and C02 Used in bread beer wine and liquor production Glycolysis Key Concepts Glycolysis occurs in ALL cells Glycolysis occurs in the cytoplasm Supports that glycolysis evolved BEFORE mitochondrial endosymbionts Glycolysis has an energy requiring phase and an energy generating phase Energy needed to break bonds in glucose activation energy 2 ATP are consumed 4 ATP are produced End products of Glycolysis from 1 glucose 2 molecules of pyruvatepyruvic acid 2 molecules of ATP net gain 2 molecules of NADH Glycolysis requires NAD to occur NAD is regenerated differently in the presence vs absence of oxygen Fermentation Key Concepts Glycolysis requires NAD to occur ln aerobic conditions NADH is converted back to NAD by releasing electrons to the ETC For electrons to flow through the ETC their must be 02 available to receive them at the end In the absence of 02 cells need another way to regenerate NAD Cells use fermentation to convert NADH back to NAD Fermentation does NOT produce ATP The waste products of fermentation vary depending on the type of organism Many products of fermentation are used in food production by humans Tutorial 19 Energy Ill Kreb s Cycle and Electron Transport Kreb s Cycle Key Concepts The Kreb s cyce occurs in the matrix of mitochondria Pyruvate is converted to Acetyl CoA before entering the cycle This conversion produces 1 NADH and 1 C02 per molecule of pyruvate The C02 we exhale is produced by the Kreb s cyce For each molecule of Acetly CoA entering the Kreb s cycle 3 NADH 1 FADHZ 2 C02 and 1 ATP are produced Electron Transport Chain Components of the ETC are embedded in the inner membrane of mitochondria Electron carriers NADH and FADH2 are oxidized back to NAD and FADH Oxidation causes them to release the electrons they are carrying to components of the ETC Each component of the ETC is more electronegative Pus the electrons toward it so electrons move between components spontaneously without added energy Larger differences in electronegativity between components the steps of the ETC release more energy 02 is the terminal electron acceptor this is why we inhale 02 High electronegativity of 02 allows maximal release of energy for harnessing CulpwighIEI Thu quotaerHill CDIHFIll Iil l IHEM ani inn mcpinnd Inr mpmdualinn ordinphy l l39 f im i ll w 1 r V i39 quot a 39 391quot E 7 39 39r39rv quot quot a m 39I i quot quotH 1a 3 in 1 j 39I I si to l I I i I 1 VI 1 D lt Is a in II39 I i if c in 31 n 153 ii I 7 V x 7 Inquot n l 39 so i i i c v e a o 75 c i 739 I i 7 V 7 I ll Oxidative Phosphorylation Key Concepts The movement of electrons from electron carriers NADH and FADHZ to progressively more electronegative components releases energy Release energy used to power active transport H ions out of the mitochondrial matrix into the intermembrane space This createsmaintains a gradient of H ions potential energy H diffusion back into the matrix is facilitated by ATP synthase H diffusion releases energy that is used to power the formation of ATP cytos l Tutorial 20 S39ubst ratellevell Substratelevell Ditid tive phasphuwlaiiilon phosphnwlalion phosphiawlatia v j h mmmu Photosynthesis The LighDependent Reactions Photosynthesis Photosynthesis is comprised of two processes The lightdependent reactions The lightindependent reactions The Calvin Cycle Lightdependent reactions produce ATP amp NADPH reduced electron carrier The lightindependent reactions produce Glucose sugar The ATP and NADPH produced in the lightdependent reactions DO NOT provide energy for cellular functions They only provide energy to produce sugar Sugar made in the leaves is transported to the rest of the plant Sugar is brokendown in cells thru cellular respiration to produce ATP to power cellular functions Energy from sunlight is used to produce sugars ATP and NADPH from photosynthesis do NOT leave cholorplastll They are only recycled between the 2 stages Energy from sunlight is transferred to electrons Series of TWO redox reactions electron transport chains harness the energy Electrons reexcited in between ETCs Captured energy used to Produce ATP Reduce NADP to generate NADPH Eloolron noooomor at 7 i 3 Pl 3 stooui nono g ii rom H31 224 U202 Pleatooy39anin 25quot Photon 39 mm Pigments in Membrane I 39Embrazn Of Thylakoids Li ht Reactions Photosystem ll Photo 9 take place in the Grana Granum one L 39 stack of 3 79311 i 53919 thylakoids v a 3 1 Grana multiple Thylalitoitil a i stacks 39ll39hylalooitl opaoo LightDependent Reactions Key Concepts Light energy excites electrons in pigments Excited electrons bounce between pigment molecules until they reach the reaction center Excited electron is passed from reaction center to ETC Electrons are replaced by the oxidationsplitting of H20 which producesreleases H and 02 as byproducts Energy released from ETC between PS and PSI used to pump H into lumen of thylakoid Diffusion of H back into stroma powers ATP synthase to produce ATP Energy from ETC after PSI used to reduce NADP to NADPH Tutorial 21 The Calvin Cycle 3 Camarr xi GEE Balirim Eycle Ii ILfirg htl rude33ml am agellum I 33 Flihull5E liElEiiEpH EFH31ERUEP EC v 1 FanE55 1 E Eliplrngph gllyEeratE Eli 1 EMS arbm m mn 7 i Ruinhm Iv 39 IPhEEEE A HEP quot l Iragameratim V 1 E E Eilyeerall ehy e 3phsphate 3m 3m an i 7 EADPEE a 1 hi phneph glymr m 31 39 39 EMAEPEPi E Elly EFEll hyn l Eaph ljh tE reap 3E PHEEE Redu lier I 39 my mania m Glynemuuehyde 3phn5phate 3 leap5a EJILEEEIIESE39 and Calvin Cycle Key Concepts Calvin Cycle occurs in the stroma of chloroplasts The energy and reducing power to make a basic 3carbon sugar molecule is provided by the ATP and NADPH generated in the lightdependent reactions in thylakoids The Calvin Cycle is where gaseous atmospheric carbon is xed into organic molecules Fixed carbon derived from C02 is the source of carbon for plants C02 is where plants obtain carbon to develop their body mass The Calvin Cycle occurs in three stages Stage 1 C02 is added to Ribulose 15 bisphospate Rqu by the enzyme Rubisco This produces 2 x 3carbon molecules Stage 2 Reduction Stage 2 ATP is hydrolyzed and NADPH is oxidized to be able to reduce the molecules to form Glyceraldehyde 3phosphate G3P One molecule of G3P leaves the cycle for every 3 molecules Of C02 6 molecules of C02 are needed to produce 1 glucose 12 ATP and 12 NADPH are needed to produce 1 glucose Stage 3 Regeneration of Rqu Stage 3 the remaining 5 molecules of G3P are converted into 3 molecules of Rqu 3 ATP are hydrolyzed to power this conversion Sugars produced by the Calvin Cycle are transported to the rest of the plant Once transported they can be broken down in cellular respiration to produce ATP Exam 4 Tutorials 2229 Tutorial 22 Plant Evolution and Diversity Nonvascular Plants Features of Plants Chloroplasts Photoautotrophs chorophy b Store carbohydrates as starch Cell wall made of cellulose Sexual life cycle alternation of generations Gametes zygotes and embryos protected in parent tissues gametangia Alternation of Generations Diploid forms Sporophytes produce haploid spores through meiosis which develop into multicellular haploid structures Gametophytes through mitosis Gametophytes produce haploid gametes by mitosis which join with other gametes fertilization to form multicellular diploid sporophytes through mitosis Seen in some algaes and ALL plants Evolution of Land Plants Gametangia Waxy cuticle Vascular tissue allows plants to transport material aids in support contributes to increase in size Pollen Seeds Flowers and fruits Increase fertilization using other species as pollen carriers Fruit aids in dispersal Major Groups of Plants Nonvascular plants Vascular plants Vascular seedless Flowering plants NonVascular Plants quotBryophytesquot Not a monophyletic group Small size low growing Live in moist habitats No vascular tissue so no true leavesroots Rhizoidssoil anchoring Nutrients diffuse into cells Life cycle Flagellated motile sperm Gametophyte is prominent stage Tutorial 23 Plants ll Vascular Seedless Plants and Gynmosperms Vascular Tissue Advantage Vascular tissue reduces the problem of desiccation and allows for larger growth Require water for reproduction agellated sperm Not a monophyletic group Seedless Vascular Seedless vascular plants sporophyte and gametophyte live independenUy Homosporous spores produce one type of gametophyte gametophyte produces sperm AND eggs ie ferns club mosses horsetails Seed Plants Gymnosperms Reduced gametophyte that is dependent upon the sporophyte Pollen protects sperm from desiccation and facilitates dispersal some still have sperm with a agella Seeds protect embryo from desiccation and facilitate dispersal naked lack ovary Wood cellulose and lignin mainly xylem Fewer than 750 species today Four phyla probably not monophyletic Cycads and Ginkgos Flagellated sperm swim within pollen tube Sexes separate dioecious Gnetophytes Non motile sperm Double fertilization Conifers Nonmotile sperm Male and female cones on one tree most are monoecious Mostly evergreen many have needlelike leaves Tutorial 24 Plants Ill Flowering Plants Angiosperms Angiosperms are the dominant land plant Angiosperms Seed completely protected within ovary enclosed Flower is reproductive structure modi ed leaves Perfect both male and female parts Imperfect either male g female parts Fruit protect seeds and help them to disperse Many species take advantage of animals for pollination and seed dispersal including humans The ower is believed to be largely responsible for the success of angiosperms Double Fertilization Eigma Petal Microspore Two haploid 7 N sperm nuclei I i x r r Meg Carpal 31313 i a a j Anther a S i v l l Stamen p0 re agar Ly f Filament one E quot f haploid egg nucleus and nuclei One Sperm 1 two haploid polar 39 egg embryo 2N One sperm 2 polar nuclei endosperm DW39E Sepal 3N nourishes embryo Pollen l amounts of pollen 3quot Small inconspicuous owers Plants must grow close together Trees oaks and grasses Animals carry pollen Requires large Seeds Seeds protect and nourish developing embryos Seeds of owering plant are contained within a fruit Fruit Dispersal Wind Water coconuts oat Animals Tutorial 25 Mendel and Modern Genetics Character Feature of an organism that has multiple variants among individuals Can be inherited of acquired ie ower color Trait a particular variant of a characteristic ie purple or white ower Law of Segregation 0 Within an individual alleles for a trait separate during gamete production 0 Each gamete only receives ONE of the two alleles Law of Independent Assortment During gamete formation the alleles for different traits separate independently of one another 0 Different genes separate independently because non homologous chromosomes separate independently during meiosis Tutorial 26 Genetics ll Punnet Squares and Probablities The number of possible gametes 2n where n the of HETEROZYGOUS genes Rule of Multiplication To determine the probability of an event occurring determine the individual probabilities of each independent event and then multiply the individual probabilities to obtain the probability of these events occurring together Rule of Addition if an event can occur in more than one way the probability of that event occurring is equal to the sum of the probabilities of each way the event can occur Tutorial 27 Genetics Ill Complex Expression Patterns of Multiple Alleles Complete dominance heterozygote indistinguishable from homozygous dominant Incomplete dominance heterozygote has an intermediate phenotype that is between the two parental traits ie white and red make pink ower Codominance heterozygote has unique phenotype fully expresses both parental traits simultaneously ie white and red have both red and white ower 0 Multiple alleles for a characteristic Human ABO Blood Group has Multiple Alleles Alleles encode enzymes that add carbohydrates to surface of red blood cells RBCs 3 alleles IAIBi lA encodes enzyme that adds sugar A lB encodes enzyme that adds sugar B i no enzyme sugar not added 4 different phenotypes possible Type A B AB O Blood Type O has amp sugars added to surface Only possible if BOTH alleles are ii Pleiotropy One gene effects multiple characters Indicates that product of gene has multiple uses for different purposes OR that product of gene affects something widely distributed in the organism Pleiotropic genes include Albinism mutation in one gene impacts color of eyes hair and skin Sicklecell Anemia Cystic Fibrosis mutation in one gene impacts function of lungs liver pancreas sweat glands Epistasis Expression of one or more genes is dependent on the expression of another gene Hierarchy in process of gene expression Often seen in fur color of animals The gene that is required for the expression of the other gene is epistatic to the other gene If gene A is required for expression of gene B then gene A is epistatic to gene B ie have to have hair to have hair color Polygenic lneritance Many genes contribute to one character Creates gradient of phenotypes among individuals in a population Often called quantitative traits ie skin tone Tutorial 28 Genetics IV Pedigree Analysis Pedigrees Pedigrees can also be used to infer which members of a family are heterozygous For recessive traits heterozygous individuals are considered carriers They quotcarryquot the recessive allele but do not express it observany in their phenotype Two carriers can have children that express the recessive phenotype Important to identify carriers of disease alleles Provide information whether a trait is dominant or recessive Genotype of individuals Cystics Fibrosis Recessive disease Mutation results in desiccation of mucus surrounding cells particularly in lungs and intestine CF is pleiotropic one gene affects many Leads to dif culty breathing respiratory infections reduced nutrient absorption from food Heterozygote Advantage Disease alleles are usually very rare in populations negatively impact tness CF has high frequency for a disease 1 in 25 Caucasians are carriers about 25 of the population Suggests there must be bene t of disease allele to heterozygous individuals Otherwise allele would be removed via natural selection Bene ts from having a single cope of an allele while two copies is deleterious heterozygote advantage Hypothesized that CF allele helps protect against tuberculosis TB Phenylketonuria PKU Recessive disorder Alleles encode nonfunctional enzyme Prevents conversion of the amino acid phenylalanine to tyrosine Affected individuals have low tyrosine and accumulate phenyalanine and its metabolites Accumulation causes mental retardation Neuronal damage can be prevented by eating phenylalanine free diet Newborns screened for PKU shortly after birth Tutorial 29 Genetics Part V Sex Chromosomes and Sex Linked Traits Most chromosomes are autosomes two copies of each chromosome Sex Chromosomes carry genes that regulatecontrol sex determination Because males and females have different characteristics the genes encoding these characteristics are different for males vs females Sex chromosomes are NOT homologous Sex Determination in Humans Development of Male sexual organs is driven by the presence of a Ychromosome Y chromosome carries the gene for SRY also called TDF SRY sexdetermining region Y protein TDF testisdetermining factor Presence of SRYTDFYchromosome primary factor for determining maleness during development Initiates chain of events that lead to development of male sex organs Other genes also involvedrequired Not all are on the Y chromosome Some genes involved in maleness on autosomes XY Males will ALWAYS express the allele they inherit Males are hemizygous they have only one allele so that allele will be expressed in the phenotype whether it is dominant or recessive Hemophilia X linked Recessive Trait Hemophilia is a bloodclotting disorder Mutation in proteins that form blood clots prevents normal clot formation Results in uncontrolledunstoppable bleeding Can cause organ and tissue damage 1 in 5000 male babies in US are born with hemophilia XChromosome Inactivation Males have one X chromosome and females have two Females have twice as much dosage of each gene as males Both males and females develop normally despite imbalance in chromosomes Balance of gene expression restored due to Xinactivation In cells with more than one Xchromosome one X chromosome is used for geneprotein production any others are inactivated Sometimes visible phenotype ie calico cats Exam 5 Tutorials 3036 Tutorial 30 Chromosome Behavior and Gene Linkage During prophase I when homologous chromosomes pair and line up they may swap genetic material called quotcrossing overquot Recombinant chromosomes chromosomes with swapped genetic information Mainly a random process Linked genes genes located on same chromosome tend to be inherited together Closer the genes are higher probability to be inherited together Does NOT follow Mendel s inheritance Linkage map shows sequence of genes along chromosome Map units distance between genes Tutorial 31 DNA Replication DNA Replication takes place during Sphase quotsemiconservative replication because each newly formed DNA strand has one original and one new strand of DNA origin of replication where DNA replication begins helicases unwind the DNA double helix singlestrand binding proteins keep the strands separate during replication primases iniate replication DNA polymerase adds nucleotides to the unwound parent molecule Polymerase can only add nucleotides to the 3 end of synthesized DNA Creates a leading and lagging strand Only works at the replication fork Lagging strand started using a primer to create a free 3 end Okazaki fragments short segments of DNA Ligase attaches okazaki fragments Mistmache repair removing incorrectly paired nucleotides Excision repair removal of damaged nucleotides Mutation permanent change in an organism s DNA lil i primase c ENE primer Nilt Iliasw DNA Ply39nrlerase Fellini I ll min in in I Elicia liti fraing it 54 lllllllll j Dilllift Polymerase Ful l r r r Helicase 7 c Topping merase Single strand Binding preteins 3quot r maraldireetimreplmatinn i n Helicaaes HA Polymerase Singleuzs39tnd r inding retain P m dig g DNA nlymerase I M synthesiwa IFI EHDFE u segments on lagging strand Hazard Mir L a Fragments Tutorial 32 Gene to Protein Central Dogma DNA codes for the synthesis of proteins through transcription and translation DNA template strand is used to make mRNA m RNA is complementary to DNA template and same as the coding strand of DNA Transcription occurs in the nucleus rRNA combines with proteins to form ribosomes anticodons are complementary to mRNA translating quotmaking the proteinquot 3 stages iniation elongation termination Tutorial 33 Genes in Population Population group of organisms that are members of the same species Species group of potentially interbreeding individuals that ccan produce fertile off spring Gene flow individuals can move between popuations Gene pool reproductive isolation from other species changes in allele frequency indication evolution Tutorial 34 Genetic Change in Population Genetic drift change small populations experience more Bottleneck effect event that decimates a population and leaves only a few surviving individuals Founder effect when a few individuals become geographically separate Gene flow coming and going of newold genes Mutations cause small changes in allele frequencygtlltgtllt Tutorial 35 Genetics and Natural Selection Fitness reproductive success Natural selection describes how a population overtime adapts to its environment Can only act on available phenotypic variation Can only adapt organisms to the environmental conditions at that time Random Organism does not choose just happens Stablizing selection favors intermediate phenotypic variants vs extreme phenotypic Directional selection favors individuals with phenotypes that are on one end Diversiftying selection disruptive selection favors individuals at both extremes of phenotypic range Balancing selection maintains dynamic state of balance between advantageous and disadvantageous alleles quotheterozygote advantagequot Frequencydependent selection common with predator and prey Sexual selection describes the acquisition or selection of a mate based on a speci c heritable trait Sexual dimorphism differences between males and females ie peacocks Tutorial 36 What is a Species Biological species concept a species is a group of individuals who interbreed or have potential to interbreed in nature When individuals of a population become suf ciently different to lose ability to interbreed new species has arisen Morphological species concept group of organisms that are consistently and persistently distinct from other groups of organisms and distinguishable by their morphology ie if they appear different they are different phylogenetic species concept groups organisms based on shared unique evolutionary history Prezygotic barrier barrier blocks fertilization habitat two species use different habitats timing temporal species mate different times of the year behavior exhibit different behaviors gametic literal gametes do not form zygote mechanical diffreences in shape and size of genetalia prevent successful mating Postzygotic barrier individuals from two species are capable of producing zygote offspring are incapable of growthreproduction Reduced hybrid viability hybrids between two species fail to develp or develp to sexual maturity Reduced hybrid fertility interbreeding between two species occurs but hybrids are sterile ie mule Hybrid breakdown hybrids are capable of reproducing but offspring have reduced fertilituviability Speciation when new species arise Allopatric speciation populations become isolated physically isolated Sympatric speciation populations become isolated not physically isolated Polyploidy union of two unreduced gametes


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