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Ch 1,2,3,5.docx

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York University
BIOL 1000

CHAPTER ONE: LIGHT AND LIFE Intro Cataracts = lens becomes more opaque, denaturation of protein that make up the lens The Physical Nature of Light  Energy source indirectly/directly sustaining life  Provides info for organism about physical world around them  Electromagnetic radiation = hydrogen converted to helium by the sun into EN, travels in wave form  Variable Wavelength = distance btw 2 peaks (nanometers 10^-9)  Light = part of EM spectrum detected by human eye (400nm – 700nm) (narrow)  Photon: energy packet, no mass, absorbed by electrons  Particle-wave duality = Property of light that is both a wave and stream of photons  Wavelength and photon energy inversely proportional  R < O < Y < G < B < I < V  Photon hits object  reflected OR transmitted OR absorbed (for energy/info use)  Absorption = only when photon energy equals EN difference btw GS and ES of electron  Excited state e- reps energy required for photos and vision  Pigments = class of molecules efficient at absorbing photons (chlorophyll a and indigo)  Pigments have covalently bonded C atoms in alternating single/double bonds (conjugated system)  Results in delocalization of electrons  Can interact with photon bcuz of no close bonding with any atom  Pigments absorb different wvl bcuz of differing excited states of electrons  Pigment colours comes from lights that is does not absorb (reflected) Light as a Source of Energy  Light absorbed by plants to convert CO2 into carbs  Photon absorbed electrons excited pigment captured excited e- energy ETC NADPH and ATP synthesized NADPH + ATP consumed in Calvin cycle CO2 converted to carbs  Cell resp breaks down carbs + other molecules to release ATP  Archaea Halobacterium = pigment-protein complex bacteria rhodopsin functions as light driven H+ pump, photons needed to drive pump are captured by the pigment, resulting difference in H+ conc across plasma memb reps source on EN used by ATP synthase Light as a Source of Information: Light used to sense environment Rhodopsin, the Universal Photoreceptor  Photoreceptors: molecule that absorbs light and generates a response  Rhodopsin: Opsin protein in rhodopsin binds single pigment protein retinal  Memb proteins spanning multiple times forming a complex with the retinal molecule at the centre OPSINS: MORE DETAIL!!!!  Photon absorption retinal pigment changes shape opsin alters intracellular ion conc electrical signals sent to brain  Photoreceptor cells (rods and cones) line the retina Sensing Light Without Eyes  Plant algae, invertebrates and some prokaryotes sense light without eyes  Eyespot = light sensitive, 1UM diameter, found in chloroplast, two layers of carotenoid rich lipid globules, focus direct incoming light into photoreceptors  200 diff proteins used to assemble eyespot  Eyespot photoreceptors sense light direction + intensity  C.reinhardtii – respond to light, swim towards or away from light source w/ flagella (phototaxis)  Allows cell to stay in optimal light and maximize photosynthesis light capture  Signal transduction pathway – light triggers ion conc change (K+, Ca-) and general electrical events to change flagella beating pattern  Phytochrome - plant photoR imp for photomorphogenesis, activated when seedling exposed to light  Seedling exposed to WL makes phytochrome active initiating signal transduction pathway that reaches nucleus and nucleus activates protein coding The Eye  Light absorbed and signal interpreted and visual detail developed in brain  Ocellus = simplest eye, cup/pit lined with upto 100 photoreceptor cells, sense levels of light  Photoreceptor cell = modified nerve cell with 1000s of photoreceptor molecules  Flatworms: info sent to cerebral ganglion from eyes for worms to find dark and avoid predation  Compound eyes = 100s of ommatilda units, collectively form an advanced mosaic of an image  Single lens eye = light enters transparent cornea, lens concentrates light onto photoreceptors at back of eye in the retina and the retina sends info to the brain through the optic nerve  Simple primitive eye - starting with light sensitive skin (2000 changes over 500 mill yrs!) The Uniqueness of Light  Visible light is most dominant form of EM waves on earth, most EM energy (400-700nm)  Shorter WV absorbed by ozone, destroys chemical bonds in molecules  Longer WV absorbed by CO2 and water vapour, wouldn’t supply energy for e- excitation,  Photo oxidative damage = excess light absorbtion, excited e-s react with O2, damage proteins  Too much damage can lead to death of photoreceptor cell UV Light is Particularly Harmful  Shorter UV protected by ozone O3 (UV photons react with O2)  Plants can withstand more damage…repairs do occur every 20 minutes or so  UV = ionizing radiation bcuz strong photons can remove electrons from atoms resulting in ions  Can disrupt DNA double helix (dimer=two side bases covalently linked) (enzyme used to fix dimers) Melanin, Suntanning and Vitamin D  Melanin made to protects cells from harmful UV, absorb UV dissipating 99% as harmless heat  Spectrophotometer= measures which UV rays are absorbed (absorption spectrum)  Melanocytes synthesize melanin, more melanin leads to more sun exposure (tan)  We all don’t have high melanin because humans still need UV radiation to make vitamin D Circadian Rhythms/ Biological Clocks  Circadian rhythm- not driven by daylight detection, but by a biological (circadian) clock  Sleep/wake cycles, body temp, metabolic processes, cell division, hunting, mating, hormones  Run independently of external conditions (“free running phenomena”)  Built around clock genes/proteins with autoregulatory expression  Enhances survival chances, ability to predict change in surroundings  DNA replication proteins work at night o prevent UV damage  Enable organism to keep track of season (flowering, leaf dormancy, fur colour change, migration, hibernation, sexual behavior change)  Suprachiasmatic nucleus - brain part that sets peripheral biological clocks in the body, receives light info through optic nerves  Jet lag – travelling rapidly across time zones, circadian cycle out of sync with external environment  Jet lag causes lack of appetite, fatigue, insomnia, mild depression Role of Light In Behavior and Ecology  Pigments come from carotenoids (in food) before depositing in feather, more colour = better health  Melanin (brown, darker) and psittacofulvins in parrot colours  More plant colour = more pollination attraction (pollen goes from anthers to stigma for fertilization)  Birds and insects use pollen for food (protein rich)  Camouflage – hiding in nature, tricking predators, catching prey, change in pattern/colour/behavior Ecological Light Pollution  Due to artificial light, disrupts nocturnal animals,(-) for migrating birds, bats/geckos get more pre Life in The Dark  Lost vision, eye photoreceptors (only rods) remain functional but brain image dead,  Larger eyes = better vision (nocturnal, deep sea animals, blind mole rats)  Bioluminescence – chemical energy in form of ATP released as light, 5% lost as heat, reasons are mating/preying/camouflage/communication (bacteria, algae, fungi, fish, squid, insects) CHAPTER 2: THE CELL OVERVIEW Cell Theory 1. All organisms are composed of one or more cells 2. The cell is the basic structural and functional unit of all organisms 3. Cells arise only from the division of pre-existing cells Visualizing Cells  Three domains of life: Eukarya, Bacteria, Archaea  Microscopy - technique for producing visible images of objects too small to be seen by the human eye  Light microscope (use light), electron microscope (uses electrons/better resolution)  Magnification – ratio of the viewed object to its real size  Resolution – min. difference in which 2 pts can be separated and still seen as 2 pts  Shorter wavelength = better resolution Why Are Cells So Small? (change in SA: Vol)  Vol is amount of chemical activity in cell, SA is amount of substance exchange in/out of cell  Doubling diameter = vol x 8 and SA x 4  Surface area becomes insufficient to maintain adequate exchange for its entire volume  Some cells increase exchange by flattening or developing folds/extensions Central Cell Region  Contains DNA (hereditary info), proteins maintaining DNA structure and enzymes making mRNA  Cytoplasm - All parts between plasma memb and central region. Signals, conversion of chem/light energy, make growth/reproduction molecules  Organelles – small organized structures important for cell function  Cytosol – aqueous solution with dissolves ions and organic molecules  Cytoskeleton – protein based framework of filaments (support shape, role in division) Cell Forms  Eukaryotes – DNA with membrane bound nucleus, functional organelles, extensive cytoplasm  Prokaryotes – lacks a nucleus, has a nucleoid (no membrane from cytoplasm) Prokaryotic Cells  Shapes: spherical, rodlike (E.coli), spiral  Nucleoid – highly folded mass of DNA with genetic info (unfolded single circular molecule)  DNA RNA mRNA rRNA tRNA Protein  Ribosome – 2 subunits made from rRNA + proteins  Cell wall - physical protection, rigidity, extra layer  Glycocalyx – capsule/slime, some bacteria have it, layer of polysaccs around cell wall, protects from extreme temp, antibiotics, viruses, antibodies and desiccation  Plasma membrane – converts food molecules/light into ATP (most cell functions occur)  Some archaea/bacteria have extensive internal memb structures (internal sacs from plasma memb)  Photosynthetic bacteria – complex layers of intercellular memb where photoS occurs  Most bacteria have single, circular DNA in nucleoid, some have plasmids  Gram-Positive Bacteria: single, thick peptidoglycan layer  Gram-Negative Bacteria: thin peptidoglycan sheath surrounded by outer membrane  Archaea – extreme environments, diverse metab, similar to bacteria, has some euk qualities too  Cytoskeleton filaments – shape, support, division, polarity  Pili/pilus – hairlike protein shafts extending from cell to attach to other cells Eukaryotic Cells 4 major groups – protists, fungi, animals, plants Eukaryotic Organelles + Membrane  Organelle functions are energy metabolism, molecular synthesis, storage/transport  Cytosol – solution surrounding organelles, helps with support, motility, energy, synthesis  Plasma memb proteins – transportation, receptor molecules, labeling proteins  Cell wall for platnts, protists and fungi Eukaryotic Nucleus  Nuclear envelop – separates nucleus/cytoskeleton, double memb with space in between  Lamins – protein filaments reinforce inner surface of animal cells  Nuclear pore complex – large, octagonal, cyndrical proteins, in nuclear envelop (nucleoporins)  Exchanges stuff between nucleus and cytoplasm (selectively permeable)  Nuclear pore – channel through the NPC, helps large molecules to pass  Transport protein shuttles cargo through a nuclear pore  Nuclear localization signal – short aa sequence on special proteins to get through to the nucleus o Protein in cytosol recognizes and binds it to the NPC  Nucleoplasm – liquid/semi-liquid substance in the nucleus  Chromatin – proteins + DNA, fills most nucleus space (linear DNA molecules)  Chromosome – one complete DNA molecule + proteins  Nucleoli – masses of fibres/granules, form around rRNA genes  Inside Nucleolus – rRNA genes rRNA molecules combine with proteins (ribosomal units) exits through NPC enters cytoplasm joins mRNA to make ribosomes Eukaryotic Ribosomes  Small/large subunits, 4 types of rRNA, 80+ proteins  Some are freely suspended in cytosol, others are attached to membs  Cytosol ribos – may stay, enter nucleus, become parts of mitochondria/chloroplasts/cytoskeleton  Nucleus ribos– may join chromatin, line the nuclear envelop or remain in nucleoplasm  ER – many ribos attached, proteins follow special path to other organelles Endomembrane System  Internal inter-related membranous sacs that divide the cell into structural/functional compartments  Protein synthesis/modification, protein transport, lipid synthesis, detoxification  System connected physically/indirectly (vesicles)  Vesicles – small memb bound compartments that transfer substances  Includes… nuclear envelop, ER, golgi complex, lysosomes, vesicles, plasma membrane Endoplasmic Reticulum  Interconnective network of membranous channels/vesicles called cisternae  Cisternae – single memb surrounding closed space called ER lumen  Rough ER has ribosomes on surface  Final protein folding + modifications in ER lumen go in small vesicles that pinch off ER travel through cytosol join organelle/golgi complex  Smooth ER has no ribosomes on surface o lipid synthesis for cell memb turns toxins/drugs into more tolerable for the body  RER/SER are connected  Proportions of ER in a cell reflect activities  Enzyme making cells = more RER, less SER  Lipid synthesis/toxic breakdown cells = more SER, less RER Golgi Complex  Stack of flattened membranous sacs  More protein secretion from cell = more golgi complexes  Proteins come from ER  Cis faces nucleus / trans faces plasma memb  Vesicle contacts Cis and fuses with golgi memb  contents released in cisternae chemical protein modifications (functional groups, lipids, carbs, removing aa parts)  proteins transported within golgi to trans sorted into vesicles that bud off from golgi  Regulates movement of proteins  “Postal codes” added to the proteins for their destinations  Some vesicles exit through exocytosis (signaling molecules, hormones, waste, enzymes)  Vesicles fusing with the plasma memb become a part of it (expands cell surface)  Endocytosis – opposite of exocytosis, pinches inwards Lysosomes  Small membrane bound vesicles with hydrolytic enzymes  Digests protein lipids, nucleic acids, polysaccs) (molecules subunits recycled)  Only for animals (vacuole for plants)  PH = 5 (cytosol pH=7.2), enzymes function better, reduces risk to cell if enzymes are released  Digest food and dysfunctional organelles (autophagy)  Phagocytosis results in lysosome fusing to a vesicle with engulfed materials (white blood cells)  Lysosomal storage disease (genetic disease) where 1 type of hydrolytic enzyme is missing and substrate accumulates to interfere with normal cell activity (Tony-Sachs) Mitochondria  Membrane (double membrane) bound organelles in which cell respiration occurs  Cell resp – organic molecules broken down into H2O/CO2, energy released/captured (ATP)  Require oxygen  Outer mitochondrial memb – smooth, covers outside  Inner mitochondrial memb – surrounds mitochondrial matrix, expands SA with folds  Mitochondrial matrix – contains DNA/ribosomes (evidence of endosymbiosis) Cytoskeleton  Interconnected system of protein fibres + tubes extending through cytoplasm(shape/organization)  Most developed in animal cells  3 types: microtubules, intermediate filaments, microfilaments  microtubules/filaments are constantly being disassembled and reassembled elsewhere in the cell  plant cell have only microtubules and microfilaments while animal cells have all three Cytoskeleton: Microtubules  Largest component, made from tubulins (proteins), Wall of 13 protein filaments side by side  Dimer – one a-tubulin/b-tubulin subunit noncovalently bound together (filament=linear dimer poly)  Provid
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