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Biology 1000 Chapter notes

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BIOL 1000
David Stamos

Biology 1000 Chapter Notes 1. Light and Life Why it matters:  Impressionists used unmixed colors on a canvas next to each other so that the colors would “mingle” and create the impression of another color  They would try to capture the momentary effects of sunlight and the changing color of a scene by painting outside  Later in the years Monet’s works became more dull and muted from his previous vibrant works and he used more red-yellow colors in his later works  Later Monet realized that it was not his style that had changed  He suffered from cataracts (vision deteriorating) and the lens of his eyes became more opaque  The cause is the denaturation of a protein within the lens and this opaqueness causes his eyes to decrease the transmittance of blue and therefor in his eyes everything looked more yellow and thus his painting were more yellow as well The physical nature of light:  Light has two important functions: o 1. It is a source of energy that sustains all life o 2. It provides organisms about the physical world  Some organisms such as the green algae C.reinhardtii use it for both energy and information  The algae have a large chloroplast that use the light for photosynthesis to make energy rich molecules  The cell also contains an eye spot that senses the intensity and direction of light  Regardless of which the organism use, the organism still needs to capture the light What is light:  The reason why there’s life on earth is due to the distance from the earth to the sun  The sun converts about 4 mil tones of matter into energy every second and send is given off as electromagnetic radiation that travels at the speed of light and reaches the earth in about 8 mins  Electromagnetic radiation moves in the form of two waves, one electric and one magnetic and they are perpendicular to each other (90˚)  The wavelength of an electromagnetic radiation can range from less than a Pico meter or more than a kilometer and scientists use this to distinguish b/w the electromagnet rad.  Light can be defined as the electromagnetic radiation that humans can detect with their eyes  We can see from 380nm (purple) to 750nm (red) anything outside we cannot see and its either ultraviolet or infrared  It is hard to characterize light since it can be described as a wave and also as a stream of energy carrying particles called photons  Amount of energy in a photon is inversely related to the wavelength  As there is a shorter wavelength, the photons contain more energy and vice versa  Many (about 10^21) photons hit every square meter of the earth’s surface Light interacts with matter: o Light can interact with and change matter o These changes allow the light to be used o Photons will either be transmitted through, reflected off, or absorbed by the object it hits it o For most objects all three come into play when contact is made o For the photons to be used by an organism it needs to be absorbed o The organism have molecules called pigments that can absorbed light o There are many pigments that absorb different wavelengths of light (different colors like blue and green) for example chlorophyll a in photosynthesis, retinal for vision, and indigo that gives the blue color of our jeans o What makes pigments capture light? : all the pigments have a similarity, they all have a region of covalently bonded carbons with alternating single and double bonds and this arrangement is called a conjugated system o This creates a delocalization of electrons that allow the molecules to interact with the photons Why chlorophyll is green:  Absorption of light occurs when a photon transfers its energy to an electron of the pigment molecule  All the electrons are in ground state (0) and once the photon transfers its energy, the electron will be excited to a higher energy level  Chlorophyll molecules only have two higher energy levels, one when red light excites it to level one and blue light that excites it to level two (blue photons have more energy)  Two important principles of light absorption by pigments: o 1. A photon can excite ONLY ONE electron to higher energy state o 2. The energy difference between the state of the excited electron and ground state must MATCH the energy of a photon  If the energies don’t match the photon isn’t absorbed and thus blue or red photons match perfectly so the photons are absorbed  Chlorophyll is green because it absorbs blue and red photons and doesn’t absorb green ones therefore the green photons are transmitted or reflected and we see the green color and therefore we see plants as green  The effectiveness of light that is used to carry out biological processes varies depending on the wavelength  An Action Spectrum shows the effectiveness of different wavelengths of light on a biological process  For example an action spectrum showing the rate of O2 release in Photosynth would show that in red or blue, the rates are the highest since the chlorophyll absorbs those two wavelengths  The actions spectrum on pg. 5 fig 1.8 shows photosynthesis occurs with other wavelengths too and this is b/c photosynthesis includes accessory pigments that can absorb wavelengths b/w red and blue Light as a source of energy:  The excited state electron contains a lot of potential energy that is used to synthesize energy rich compounds such as NADPH and ATP which are used to convert CO2 to carbs  Some of the chemical energy is used to synthesize other biological molecules such as lipids, proteins, and nucleic acids  Even though photons have very little energy in each one of them, the photosynthetic apparatus in a single C.reinhardtii absorbs millions of photons every second  Some organisms use light for processes other than photosynthesis  For example the halobacterium has a bateriorhodopsin which is a light dependent protein pump Light as a source of Information:  Organisms use light to sense their environment  The ability to sense light is important since it is harder to do something in the dark  Not every organism sees the world in the same way Rhodopsin, a Highly Conserved photoreceptor:  Light sensing system is a photoreceptor  The most common photoreceptor is the rhodopsin  Rhodopsin is used not only for vision (ex animals) but also a light sensing unit for organisms such as the C.reinhardtii in the eyespot  Each rhodopsin contains a protein called opsin  Opsin bind a single pigment molecule called retinal  The retinal is located in the center of the rhodopsin  Opsins are membrane proteins that span a membrane  Absorption of a photon light causes the retinal to change shape from cis to trans  This change causes the alteration in the opsin protein in which causes things such as alterations in intracellular concentrations and electrical signals  In humans and other mammals these electrical signals are sent to the brain  In the eye of a human there are about 125 mil photoreceptors (rods and cones) and each photoreceptor contains thousands of rhodopsin molecules  Rhodopsin is very common and the widespread might be because if its early development in evolution  Even though vision and smell are different, proteins similar to opsin are used in olfaction (smell) suggesting that parts of the opsin are particularly useful in sensing the light Sensing light without Eyes:  Not all organisms need eyes to detect light  For example the C.reinhardtii has an eyespot to detect light  The eyespot allows the organism to detect light direction and intensity and using the flagellum it can either swim towards or away from the light and this is called phototaxis (movement of a cell in response to light)  Phototaxis allows the cell to stay in the optimum light environment to maximize light capture for processes such as photosynthesis  When the light is absorbed by the eyespot , rapid changes in the ion concentrations occur (K and Ca) which causes some electrical events which changes the beating pattern of the flagella used for locomotion The Eye:  Animals use the eye as an organ to sense light  For vision, the animal must have a brain or a simple nervous system that can interpret the signals coming from the eye  The eye and the brain are thought to have co-evolved since the detailed visual processing occurs in our brain  Basically we actually see with our brain and not the eye since the eye only receives light and sends signals  Simplest eye is the ocellus that contains up to 100 photoreceptors  The ocellus is covered by pigment cells that block the light rays coming from the opposite side and therefore light received comes from the side the planaria is facing  They use this light detection to swim away from areas of concentrated light and go into darker areas so that they can reduce the risk of predation  This (ocelli) can occur in animals, insects and other organisms as well  The eye of a planaria is not much more advanced but the compound eye and single lensed eyes are much more advanced since they can produce an image of the environment and distinguish between shapes and objects  Compound eyes are common in arthropods such as insects and crustaceans  They have thousands of ommatidia grouped together  Light enters an ommatidia is focused onto a bundle of photoreceptor cells and the brain receives signals and from these signals mosaic images of the world is created  Compound eyes detect movement extremely well (flies can see us move therefore it’s hard to kill them)  Some invertebrates have a camera eye in which the light enters the cornea and the lens concentrates the light, then the photoreceptors at the back of the eye (the retina) records the image Darwin and the evolution of the eye: o The eye evolved through variations (mutations) and natural selection overtime o As the environment changed the eye adapted to the environment o The eye evolved a lot o According to scientists, from the simplest patch of light sensitive cells to the camera type eye has 2000 small improvement that took less than half a million years o Primitive eyes appeared in fossil 500 million years ago and therefore our eyes could have evolved 1000 times o Eye evolution occurs when it is needed for survival o Most evolution occurs due to survival o For example a predator has heightened vision, then the prey and other predators mush attain comparable eye improvements to help survive (prey) or compete (other predators) o and optically refined eye also requires an improved brain or a more advanced neural processor for the info being sent by the optic nerve Light can Damage Biological Molecules  even though light is a very small portion of the electromagnetic spectrum, it is required to sustain life on earth and is also needed for many light-driven processes such as photosynthesis  it is not a coincidence that we require such a narrow band from the E.M spectrum  light is the most dominant since the ones with shorter wavelengths are absorbed by the ozone and the ones with longer wavelengths are absorbed by water vapor and CO2  another reason why light is used is for the energy  radiation of shorter wavelength can destroy chemical bonds of molecules in living things  the shorter wavelengths would not just excite it but it would oxidize the molecule causing it to become an ion (the electron has so much energy that it jump out of the molecule)  radiation with longer wavelengths would not provide enough energy to excite the electron  Wald (scientist) suggest even on another planet, light would be used for their processes Damage by light: Direct Effects:  Light can damage biological molecules but all organisms have developed mechanisms to help prevent or repair light induced damage  A good example of light damage on a biological process is found within photosynthesis  The photosynthetic apparatus is composed of many photosystem and each photosystem takes in about 10 000 photons every second  This high energy within the core can result in damage to the protein components  The damage is unavoidable but the rapid repair of photosystems developed early during the evolution of life so that the rate of photosynthesis can be maintained even under high light conditions  Plants also have carotenoids that take in the excess light and safely dispose it as heat  Even though carotenoids are not present in great quantities like chlorophyll, plants need to synthesize them and if the plants can’t they will turn white since the chlorophyll becomes oxidized and it loses its light harvesting capabilities Damage by Light: Indirect Effects:  UV rays are accompanied with light and come to the earth  The most harmful UV ray (UV-C) is absorbed by the ozone but UV-B and UV-A reach the surface of the earth  Due to its high energy, the UV rays can randomly ions atoms in a range of molecules such as pigments or proteins  Due to the structural integrity of FNA, it is especially vulnerable to UV rays  When a UV ray hits DNA, it cause the neighboring nucleotides to covalently bond creating a “dimer”  These dimers cause it to change shape, prevents replication and stops gene expression  Cells have evolved to repair this damage but dimers can lead to genetic mutations  Melanin absorbs UV rays (300-400nm) and an Absorption Spectrum (plot of the amount of light a pigment absorbs in relation to the wavelength) shows this  Humans develop melanin in special skin cells called melanocytes  People in areas of higher sun exposure have more melanin  Melanin protects DNA from UV rays and also helps prevent skin cancer  Melanin also prevents UV rays to penetrate the skin and destroy B vitamin folate  There isn’t a high level of melanin in people because some UV is required to synthesize vitamin D which is critical for bone development  Someone from Africa living in Sweden could get Vitamin D deficiency but many foods consume have vitamin D and therefore they receive the proper amount their body needs  Natives have kept their dark skin even though they live in a sun-poor area due to their diet of fish and other marine life that have high amounts of Vitamin D Role of Light in Ecology and Behavior:  There are different environments with different amounts of light  Organisms must adapt to the light in order to survive (photosynthetic organisms must make adjustment in the light harvesting properties of the photosynthetic properties) Using light to tell time: Circadian Rhythms:  Since the earth rotates on its axis every 24 hrs., day and night is created and life has evolved to work under this constant rhythmic cycle  Many physiological and behavioral phenomena in this rhythmicity, they vary depending on the time of the day  Some processes include sleep wake cycle, locomotion, body temperature, mating…etc.  Many physiological and behavioral phenomena that’s geared to the earths day-night cycle is called circadian rhythm because it revolved around a 24 hour period  Circadian rhythm isn’t controlled by external light, it is controlled by the organisms internal clock (endogenous)  The clock is set by the external light BUT it can operate with complete darkness or fully lit environments  It is “free running” as it doesn’t depend on exposure to the sun  It is important to be able to tell when it is day and when it is night  For example a plant will photosynthesize at a maximum rate during the day due to the sunlight exposure while not performing DNA replication and protein synthesis since UV rays can damage DNA therefore it occurs during the night and therefore the DNA replication is under circadian rhythm  In most animals, the internal clock that controls these circadian rhythms is found within the Suprachiasmatic nucleus (SCN), a region in the hypothalamus  The SCN receives light from the optic nerve and sets the biological clock and the clock is used to regulate many functions such as secretion of melatonin hormone  Melatonin is thought to have a role in the sleep-wake cycle since its synthesis is active during the night and inactive during the day  Several things can interfere with circadian cycling such as jet lag  While travelling across many time zones the external light can put your circadian clock out of sync and while u should be sleeping u are still awake  Jet lag can cause lack of appetite, fatigue, depression…etc.  Circadian clock will take a few days to adjust and reset itself to the new environment and cannot instantly reset  Some plants and animals show seasonal cycles such as flowering or hibernating or migration  In some parts of the world the changes in day length (photoperiod) indicates changes in season  Plants and animals depend on the photoperiod to prepare for seasonal activities Avoiding Detection: Camouflage:  Camouflage works when one animal can’t detect another due to the background (they blend in)  Pattern and behavior are central roles in camouflage  Importance of camouflage is shown through the peppered moths : o During the industrial revolution the tree trunks that the moths (dark colored and light colored peppered moths) stayed on became very dark and so the dark colored moths were able to stay hidden better but the light colored ones were very visible, later when the trees returned to the norm light color the light colored moths were able to camouflage themselves much better but now the dark colored ones are visible to the prey, thus when the organism is camouflaged it survives better but when its visible it is easily consumed or attacked Using color as signals: o Animals use bright colors to show that they are distasteful and/or armed and dangerous o We can see these signals o For the signals to be useful the other organism must be able to see colors, if it can’t then it is useless o Some animals use other things as a signal such as the skunk smell, or a bee buzzing o Some animals may mimic other animals’ warning signals o Flowers have many beautiful colors and patterns not to attract us but to attract pollinators to carry pollen from the anthers to the stigma of the same or another flower o Plants that use animals must attract the right pollinators so the pollen and nectar is not wasted o The characteristics of the flowers (for ex shape and color) attract specific groups of pollinators o Since pollinators like different colors or receive different wavelengths, the flowers attract the different pollinators o For ex humming birds like red flowers while bees like yellow or blue flowers and can perceive UV light therefore they like the flowers that have UV-reflecting pigments Light in Aquatic Habitats:  Almost no light goes past 150 m in water  Water scatters and absorbs longer wavelengths more appropriately and therefore after 30 m only blue wavelengths are present  Red algae survive in greater depths since they absorb the blue wavelength and give off a red color  They absorb the blue wavelength due to an accessory pigment called phytoerythrin  Fish that live in shallow waters have brilliant colors while fish that live in deeper waters have a dark black top and a silver underbody which allows them to be camouflaged when viewed both from the top and bottom Ecological light pollution:  Although the invention of the light bulb is great, the street lights and many other lights that are being used create light pollution and in the US only 40 percent of the country true has dark nights  The presence of these artificial lights disrupts nocturnal animals that are accustomed to operating in the dark  For ex newly hatched sea turtles are supposed to head to the ocean because it is brighter but now with lighting on the streets and beaches they may head inland and get killed  Birds collide with lit buildings when migrating  Other animals such as geckos and bats benefit from this as more insects become present due to the light (more prey) Life in the Dark:  Humans see very well in the day but at night we lose our ability to see colors and detect shapes  Nocturnal animals like frogs and insects like moths see very well with dim light  Some animals live their whole lives in darkness  The blind mole rat lives in darkness its whole life but comes out for light once in a while but it is still blind  They have tiny eyes covered by tissues but the photoreceptors are present and can detect light while the processing part of the brain is reduced  These receptors help the blind mole rat set their biological clocks and control their circadian rhythms  The SCN of their brain still works properly receiving information from the eyes  The Mexican Cavefish is another example where the surface water one has eyes and pigment but the cave-dwelling one has no eyes and no pigments Organisms Making their own light: Bioluminescence:  Bioluminescent: produce light  Bioluminescence process is the opposite of light absorption  Chemical energy in the form of ATP excites and electron in a substrate molecule to a higher excited state and when this returns to the ground state the energy I released as a photon of light  Bioluminescence is very efficient and only 5% is lost due to heat (this is essential since high heat production is not compatible with life)  This is used to attract a mate, attract prey, camouflage, communicate, or as a defense mechanism  Unicellular algae light up when there’s a disturbance in the water or a fish is around and the fish becomes visible to its own predator therefor it leaves  Some bacteria use bioluminescence in communicating called quorum sensing but when the bacteria releases the compound it’s not enough therefore once it has multiplied and the population has grew it reaches the threshold and they can release enough of the compound to evoke a physiological response and this response activate certain genes and some of these encode for proteins required for bioluminescence  Quorum sensing is now believed to be the basis for “milky sees” (bright lit parts of the ocean)  Some fungi in the forest have bioluminescence but it is a mystery of how and why  In order for bioluminescence to work the other organism must perceive it therefore it must have a light sensing organ  From that we can say that bioluminescence came after light sensing  Most bioluminescent organism are marine and are most abundant below 800 meters where light cannot reach it 2. Origins of Life Why it Matters:  In 1984 scientists found a meteorite that they found to be from mars and was 4.5 billion years old  After analysis of the rock they determined there was life on mars at the time  They found that the rock was fractured and infiltrated by liquid water  There were structures in the fractured surface that were similar of a fossilized prokaryote  They found mineral globules that that resembled the mineral alterations caused by primitive prokaryotes on earth  They also found a lot of PAHs (polycyclic aromatic hydrocarbons) which is the compounds that forms when microorganisms die and break down What is Life?  Both living and none living things, at a molecular level, follow the same laws of chemistry and physics  Biological reactions in biotic organism are only modifications of reactions in the abiotic world Seven Characteristics that All forms of Life Share: 1. Display order: all forms of life are arranged in a highly ordered manner with the cell being the fundamental unit of life 2. Harness and Utilize Energy: all forms of life require energy that they can get from the environment to maintain their ordered state 3. Reproduce: all organism have the ability to make more of their own kind 4. Respond to Stimuli: organism can make adjustments to their structure, function, ad behavior in response to changes in the external environment 5. Exhibit Homeostasis: organisms can regulate their internal environment so that the conditions remain constant 6. Growth and Development: organism increase in size by increasing the size and number of cells, they can also change overtime 7. Evolve: organisms change over long periods of time to adapt to their environments  Viruses seem to be living things since they have many of the characteristics such as reproducing and evolving  They do have nucleic acids but they don’t have the cellular machinery to synthesize their own proteins therefore they go and take the machinery and metabolism of other living cells to reproduce o That is why viruses aren’t considered to be alive The Fundamental Unit of Life is the Cell:  Scientist found three generalizations about the organization of living things which together make the cell theory: 1. All organisms are composed of one or more cells
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