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BIOL 1000
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BIOL 1000 Light and Life: chapter 1 Lecture Notes Désirée Blondin-White Index: Class memos………………………………………………………….2 LIGHT……………………………………………………………………..2 LIGHT IN CONTACT WITH MATTER………………………..4 LIGHT AND LIFE………………………………………………..……5 ROLE OF LIGHT IN ECOLOGY AND BEHAVIOUR…….7 Circadian rhythms………………….7 Camouflage Colour as signal Life in aquatic environment....8 DARK SIDE OF LIGHT……………………………………..…….10 1 Sept 6th 2012 Cells, Molecular Biology and Genetics (With Dr. Nivillac) Grading: Test 1: 18% OCT 4 Test 2: 22% NOV 8 Final: 33% WEEK OF DECEMBER 15th Labs: 22% (each) Additional activities: 5% If you miss a lab: contact Nev within 24 hours at: [email protected] Sept. 7 2012 BIO1000 (With Dr. Gadsgen) *Italic text underlines material from Dr. Gadsgen’s lectures LIGHT AND LIFE LIGHT: -Wavelengths that aren’t absorbed bounce from object and produce the colours we see -When there are more blue molecules, more light will be absorbed and less light will be transmitted -Microbes absorb the energy absorbed by plants and they themselves can absorb the transmitted sun energy  all organisms benefit from plants’ photosynthesis as it is transmitted through the food chain. ATP are energy molecules ATP becomes ADP+Pi (phosphate) = energy ADP binds to macromolecules3D structure is changed, which allows the molecules to react by making or breaking bonds E.g: On next page, fig. 1.1 2 Macromolecules are for example: proteins, nucleic acids, etc. Structure change puts reactants in position to allow electrons or proton transfer. Structure in position to exchange protons, hence, make or break molecules. *Alpha phosphate is one closest to carbon Phosphates are a very Figure 1.1: Example of ADP, ATP structure change large group, they are negative and they form ATP, in which the create repulsion effect, which creates situation in which bond holding the two phosphates breaks (phosphoester bond) Ester: An organic compound made by replacing the hydrogen of an acid by an alkyl or other organic group ATP: the magic molecule Phosphoester: if carbon replaced phosphate, bond would become an ester Chlamydonasprotocoa (eukaryote cell) Chlamydosmonas have an eyespot called a stigma: can recognize light without seeing (senses light) This induces chemical change in all which alter’s it’s function Chemical changes in cells are called cascades: they induce a change in function. Cells moves towards the light light affects flagellin Flagellin is a structural protein in bacteria flagella Chloroplast has two inequal membranes (double membrane structure) Semi-permeable is the inner membrane Impermiable is the outer membrane The thylakoid membrane is where photosynthesis occurs What is light: It is a visual region of the magnetic spectrum 3 Light is described according to wavelength but behaves as particles called PHOTONS The shorter the wavelength, the higher the energy The longer the wavelength, the lower the energy PHOTONS: There are parts on the light spectrum that we cannot see: UV and Microwave (red and blue) LIGHT IN CONTACT WITH MATTER: Everything that absorbs light is a pigment *Carbon-ringed structures with double bonds are what absorb light best -Photons must equal electron’s energy. Eumalin: black and brown melanins Phaomelanin: red melanin, more common in women. Melanin are layer cells in the epidermis, they react to light to protect DNA from UV damage. -Melanosomes are vesicles that contain/store melanin -Melanosomes absorb lightaffects release of melanin into cell cytoplasm By absorbing light, they protect DNA from sun damage Light enduces enzyme protection from gene: change in genetic expression Vitamin D: (Cholecaciferol): made in skin @ specific light intensity: UV index of 3 (270-300 nm) recognize chemical composition draft Vitamin D is useful for healthy bones, fertility, antioxydants, fighting infections Involved as coenzyme, aiding reactions (ryn) Co-enzymes: donate protons and electrons Light can either be: -Reflected off objects -Transmitted through objects -Absorbed through the object: our eyes can absorb red, blue and green wavelengths *Unless an organism absorbs light, it cannot be used 4 Pigments are the molecules that absorb light Colour of pigment is due to what it reflects, not what it absorbs *No need to memorize atomic drafts REMEMBER: STRUCTURES ARE COMPOSED OF DOUBLE AND SINGLE BONDS: they determine what pigments will absorb light in regards of wavelength i.e of what’s a pigment: indigo, keratin LIGHT AND LIFE: Λ= lambda = symbol for wavelenght Blue light absorbed by plant : they are unable to absorb green light One red photon will excite an electron green light is REFLECTED from the plant, hence the appear green Blue and red wavelengths have higher absorbency than green wavelengths: why? Because of accessory pigments Retinual is not a protein: it absorbs light.: LIGHTStructure changeallows Protons to cross membrane Diffusion: The action of spreading the light from a light source evenly so as to reduce glare and harsh shadows. Protons go through ATP synthase: makes ATP Flagella drives bacteria to the light Light driven ion pumps* watch video Cis conformation: cis and trans are dependent on species Photosynthesis: process in which plants convert energy from sun into sugar to feed other organisms Cellular respiration: organisms release the energy stored in plants A photosynthesizing organism can be of various colours Photoreceptors: Light sensing proteins involved in sensing light and providing a response in the organism. -When photoreceptor comes into contact with light, it changes structure 5 - Protein undergoes some conformational change - Signal transduction cascade¸ CO-RETINAL: TRANS-RETINAL: Cis conformation creates ATP, affects locomotion: to allow energy production and to move away from harmful light (blue or UV lights) Phytochromes: light receptors in plants growth off the organism in response to light Positive phototaxis: organism moves towards light: moths Negative phototaxis: organism moves away from light stimulus: flatworm Light reaches photoreceptor-retina-eye (as organ)optic nervebrain Superchiasmic nucleus Flatworms (planeria) don’t have eyes but have photoreceptor cells: only permits the organism to detect light and to move to or away from it. Those eyeholes do not see, but can detect light. The eyecup blocks light and can determine the direction of light. Evolution of the camera eye (what humans have) Camera eyes are image forming and can detect colour. DNA sequence changemutationsmost mutations are badrarely, one mutation creates a more effective gene eyes are such an evolutionary case. An efficient gene allows the organism to survive in environment Environment selects for the most fit organisms detecting light allows to detect where predators may be found. Bacteira pathogens: antibiotics (ampicillin) Bu this environment selects for cells that can survive in the presence of the antibiotic selective pressure. Hospital strains: high concentration of resistant microbes= microbe adaption 6 Community strains: less resilient bacteria Selective pressure influences adaptation of bacteria: e.g: temperature If mutation occurs in DNA it does not occur in RNA  mutations are not found in human genome without natural selection: time and circumstances will tell if your mutation is useful, but it won’t show without natural selection. Superchiasmatic nucleus: production of hormones and cytokinesis affected, thereby affecting other tissues. LightretinaSCN Light has effects on melatonin production: melatonin affects sleep Retinol transforms chromoform-absorbs photons Opsinscis formvision, ion pumps, flagellar movements Flatworms have OCELLUS eyespots FLIES HAVVE OMETIVIUM eyes with many photoreceptors The ocellus eyes are adaptive -First eyes could sense light, had photoreceptors -Eye evolves: indentation to find origin of light -Eye without pupil cannot control light coming in; eye is more vulnerable. -Lens: light is focused on photoreceptors -Pupil: controls light coming in Evolutionary leftover: blind spot: adaptive: optic nerve needs to pass through Simple eyes are not less adaptive: e.g: flagella, mollusks, Pin-eyed creatures LIMPET: Simple layer of photosensitive cells. ROLE OF LIGHT IN ECOLOGY AND BEHAVIOUR: -Circadian rhythms sleep patterns -Camouflage -Using colour as signals -Light in aquatic environments 7 CIRCADIAN RHYTHMS: 24 hour cycle that influences sleep patterns Serotonin producesmelatonin Enzymes have to be expressed=made or turned-on. -Organisms have adapted to their differing circadian rhythms times. -Process continues in light due to residual activity: melatonin tends to induce sleep Plants: other molecules are affected by circadian rhythms ie: to prepare for photosynthesis -There are dark/light reactions in the cells. -Protein and other molecules are made that protect cells (DNA) from U.V damage Melatonin is made in the pineal gland. Triptophan (amino acid that makes serotonin) also makes melatonin. Melatonin shown to be an antioxidant (absorbs free radicals): may have anti-cancer effects/properties *Not a result of organism responding to result in light: Dark≠Sleep C.R set by external light Controlled by internal (endogenous) organism-based clock e.g: plants make photosynthetic prep at night so that they are ready by daylight to absorb most of sun’s energy. Organisms repair DNA at night  sun damages DNA Superchiasmatic nucleus of brain: where circadian rhythms clock is found. Mole rat: functionally blind, yet are decended from ancestors with functional eyes. They can still detect light and regulate photoreceptors and circadian rhythms. CAMOUFLAGE Co-evolution of characteristics of light: i.e: camouflage Works when one animal fails to distinguish another from the background e.g peppered moth COLOUR AS SIGNAL Signals used by animals: scent, colour, sound, but these signals are only useful if the organisms they are trying to attract or warn can see them. 8 Flower colour and pollinator: many specialized relationships between flowering plants and they animal pollinators. Coevolution: simultaneous evolutions of adaptation in two different species differs: e.g other animals may see the spider that humans cannot see in the flower LIGHT IN AQUATIC HABITATS -Water rapidly attenuates longer wavelengths (RED) of light -The deeper the water is, the less colourful the organisms are Varying characteristics of organisms in varying depths of water: Fish that are at surface have image-forming eyes Fish at the bottom do not: they are bioluminescent Luciferin reacts with oxygen to create their glow LUCIFEREN: Protein enabling bottom organisms to produce light Bioluminescence is a molecular reaction induced by light to create light GFP: Green fluorescent protein Fireflies: use enzyme called luciferase (substrate luciferin)  Requires ATP hydrolysis  Luminescent + 0₂ (g)  Proteins are used in biotechnology to track proteins in a cell: fuse luminescent genes to a gene of interest (cloning for research purposes) 9 1.DNA is attached in lab 2. GFP will fluoress when exposed to UV light 3.DNA is placed in cell 4. Gene is fused in RNA transc ription proces s 5. Translation process 6. Fused gene becomes protein 7. When UV light reaches protein, fluorescence occurs 8. One cell becomes fluorescent after mitosis: it can be traced 10 9. Means to identify specific cells that have picked-up the recombinant DNA 10. GFP is selectable mature gene IS THERE A DARK SIDE TO LIGHT: U.V rays damage DNA and RNA U.V rays cause cell mutations = formation of “dimer”: breaks DNA bonds HOW ORGANISMS AVOID UV DAMAGE: -Animals have fur or feathers= protection -Humans produce melanin and it buffers DNA damage by UV rays Melanin is produced in skin cells. Those who live closer to equator have higher levels of melanin. Albinos do not produce melanin. Too much melanin= makes one vitamin D deficient, which in turn may contribute to rickets -Some vertebrates do not see the sun, but still produce Vit D e.g: mole rats Articifial lights can affect human health: affects melatonin production Light pollution: astronomical light pollution reduces the number of visible stars. Light pollution is detrimental to birds and skylights from cities disrupt distant ecosystems. Direct damage is when light damages DNA bases Indirect damage is when protein is damaged that will eventually cause DNA damage. Max absorbance of melanin is 800nm wavelengths Chromophoretic molecules have max wavelengths that they absorb: the bases on DNA absorb UV light maximally at a wavelength of 260 nm Purity of DNA: needs to be quantified: proteins have a max. absorb. Of 280 nm: from pure sample or DNA, 260/280=1.8 which is absorbance level at 260 nm. Ratio 1.8 is pure if less, it becomes impure. To identify marked cells (GFP, etc), GFP is the selectable marker. Bioluminescence are molecular events from the cell induced by light or not…either way, they need a source of energy that produces light. 11 Quantity measure: to quantify, one needs a pure sample of DNA, if impure, other molecules are absorbing light. In spectrometer [email protected] 260 nm 1AU=50mg/ml DNA If by medical/experimental engineering, doctors insert uracil in DNA to cure cancer in patients, this is what leads to loss of hair, and sick-to-stomach kinds of ailments. C binds with G G binds with C A binds with T 12 T binds with A But in a sequence where T has been replaced with Uracil, A has nothing to bind with. DNA strand being copiedDNA polymerase makes new DNA called Nascent Strandmakes a 5’ to 3’ directionmutationinherited if not repaired *If a mutation occurs in the RNA it is not a real mutation as it cannot be inherited or transmitted. Drugs work by blocking replication, which can allow the cells to repair themselves before being transmitted. Triptophane makes melatonin These three amino acids are all related to melatonin Tyrosine production Phenylanalin Can adenine bind both with thymine and uracil? No because thymine’s extra methyl (CH3) group means that there’s an extra carbon atom with three hydrogens attached to it. Hence, this methyl group cannot make hydrogen bonds of its own (not like H and O bonds in thymine and adenine). As far a hydrogen bonding is concerned, the extra methyl group makes no difference. Adenine can bind to both Thymine and Uracil, but the enzymes that synthesize DNA like this extra methyl group and will only incorporate thymine. The enzymes that synthesize RNA prefer uracil ( Difference between nucleoside and nucleotide: a nucleoside consists of a nitrogenous base attached to a sugar (ribose or deoxyribose) but without the phosphate group. A nucleotide consists of a nitrogenous base, a sugar an one to three phosphate groups. How to make a phosphodiester bond? The H is removed from OH bond and the phosphate is now double-bonded to the O. 13 Biodiversity and Evolution Biodiversity ensures survival of life if one specific specie fails Gene variation: allows biodiversity and genetic diversity Biodiversity defined as variation in populations and genes Environment selects individuals with highest fitness and adaptive abilities H1N2common flu H1N1adapted virus Humans have adapted to the common flu: very few die from it. We fight it using antibodies off the common flu. But flu viruses can mutate drastically. Every 3-10 years, flu virus mutates drastically due to antigenic shifting: this means that it combines genes of different viruses Mutation is the basis of these adaptations: most of the population have trouble fighting off (making new antibodies against) new, more dangerous virusbig step in virus evolution, isn’t normal What is normal? Evolution proceeds gradually, slow collection of “positive” or “silent” mutations of environment/organis m- leads to better fitness, which leads to natural selection. Doesn’t affect you ability to live in environment H1H=Hemagluttinin protein (virus membrane) Nother proteins on virus (neuraminidase) H and N have different genetic forms of the genes that make for H and N. 14 Glycoproteins outside of cell (not on the inside like image seems to show) Glycolipids horizontal gene flow: picking other cells, switching their parts, recombining DNA. Most new viruses start in South-East Asia (where people usually live more closely to animals) and spreads westwards. It usually can take a year to reach N. America. Origins of Life 7 characteristics of all life forms: -Display order: arranged in a highly ordered manner with cell being the fundamental unit of life -Harness and utilize energy -Reproduce -Respond to stimuli -Exhibit homeostasis -Growth and development -Evolve *Homeostasis: internal system that regulates and balances pH, body temperature, etc. Cell Theory All organisms are composed of one or more cells The cell is the smallest unit that has the properties of life Cells arise only from the growth and division of pre-existing cells Although DNA and RNA contain the information required to manufacture a vast array of biological molecules, they cannot orchestrate the formation of an entire cell. The Chemical Origins of Life Earth is about 4.6 billion years old. If condensed in one year, each day of this 4.6 billion years would be an interval of 12.6 million years 15 The solar system formed by the gravitational condensation of matter present in a molecular cloud, which initially consisted mostly of hydrogen intense heat and pressure generated in central regions of this cloud formed the Sun It is estimated that it took 500 million years for Earth to cool to temperature that could nurture the development of life In 1920, Aleksander Oparin and John Haldane proposed that organic molecules essential to formation of life—including amino acids, sugars, and the nucleotide bases that form DNA and RNA—could have been made in the absence of life (abiotic synthesis) given the conditions and simple molecules thought to be
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