1 - LIGHT AND LIFE
Light
Portion of the Electromagnetic spectrum that humans can detect with their eyes Light, or visible radiation, is a narrow band of the Electromagnetic spectrum spanning the wavelengths in nanometers from 400nm (blue light) to about 700nm (red light) wavelengths outside this range- not referred to as light but as ultraviolet & infrared radiation 1nm = 10-⁹m
Electromagnetic spectrum
Is the grouping of all types of electromagnetic radiation according to wavelength. Ranges from very short wavelengths (gamma rays) to long wavelengths ( radio waves) Mnemonic- R met idiots via ugly X gir (radio, micro, infrared, visible light, UV, X-rays, gamma) The shorter the wavelength of the Electromagnetic radiation- the higher the energy of each photon it contains Light- represents only a small portion of the total Electromagnetic spectrum
Darwin and the Evolution of the Eye
Organs of extreme perfection Proposed that the eye that exists in humans and animals did not appear suddenly but evolved by variation (mutation) and natural selection over time from a simple, primitive eye Evolution of eye- explained by the huge advantage improved eye sight would give an organism eg The development of heightened visual ability in a predator would force comparable eye improvements in both prey and potential other predators Rapid eye development would, therefore, be critical to survival But, an optically refined eye is no good unless the brain of the organism improves at the same time, allowing for more advanced neural processing of the information being sent by the optic nerve.
Nature of Light
able to interact with and change matter. These changes allow light to be used by living things When photons of light hit an object, they have 3 fates 1) reflected off the object (by the matter) 2) transmitted through the object/matter 3) absorbed by the object/matter most objects exposed to light, all 3 processes come into play
Eye
-specialized sense organ capable of receiving visual images in the form of light, which are then sent to the visual centre of the brain Involves Vision, which is what distinguishes it from the eye of a simple invertebrate (eyespot of C.reinhardtii) The process of vision not only requires an eye but also a brain or a simple nervous system that interprets signals sent from the eye. Eye and brain thought to have co-evolved, coz detailed visual processing occurs in the brain rather than in the eye.
2 principles of light absorption by pigments
1) a single photon results in the excitation of 1 & only 1 electron in a pigment molecule 2) the energy of the photon must match the energy difference between the ground state and one of the excited states in order for the photon to be absorbed. if the energies do not match, the photon is not absorbed. In the chlorophyll molecule, the energy of a blue photon or red photon matches perfectly with the energy required for an electron to reach either the first or the second excited state
2 imp. functions of light for life on Earth
1) source of energy that sustains all life 2) provides organisms with information about the physical world Eg. Chlamydomonas Reinhardtii - uses light for both energy and information
Halobacterium
A group of prokaryotes that contain bacteriorhodopsin, which functions as a light dependent proton pump, the proton gradient being used to synthesize ATP Halobacteria are extremophiles, found in hypersaline environments like Hutt Lagoon Australia. Pink colour due to presence of bacteriorhodopsin Bacteriorhodopsin, composed of a protein and a bound pigment, Retinal
Pigment
A molecule that can absorb photons of light To be used by an organism - photons of light must be absorbed Absorption of light occurs when the energy of a photon is transferred to an electron of the pigment molecule Individual pigments differ in the wavelengths of light they can absorb Eg: some absorb only blue light, others only green light, some absorb light of a no. of different wavelengths
C. reinhardtii
A single-celled photosynthetic eukaryote, commonly found in ponds and lakes Each cell contains a single large CHLOROPLAST - that harvests light energy and uses it to make energy-rich molecules through photosynthesis Each cell contains a light sensor - called EYESPOT - allows it to sense light direction and intensity
circadian rhythm
A physiological cycle of about 24 hours that is present in all eukaryotic organisms and that persists even in the absence of external cues. Many physiological & behavioral responses geared to Earth's day-night cycle are called CR, because they oscillate with a period of about 24 hrs They are not direct responses to changes in the external light environment but are controlled by an internal(endogenous), organism-based clock. This biological clock is set by external light environment, but it can run a long time without any input from outside the organism. CR are free running without any input from the sun. In humans, daily fluctuations in hormone levels are controlled by a circadian clock & will occur even if a subject is placed in conditions of constant light or darkness CR found in all forms of life, from single-celled bacteria to plants and animals Being able to keep track of day/night, allows organisms to anticipate when a process occurs most efficiently during the 24 hr day & prepare Eg, in photosynthetic organisms, many proteins needed for photosynthesis are synthesized before dawn, which allows photosynthesis to occur at maximum efficiency during the daylight Thought that, CR originated to protect replicating DNA from the damaging UV radiation during the day. Thus, the process of DNA replication is under circadian control & in many organisms occurs only at night Central biological clock controlling many circadian rhythms, is found in the SUPRACHIASMATIC NUCLEUS, a region of the brain within the hypothalamus. The SCN receives light inputs directly from the eye via the Optic nerve, which it uses to set the biological clock. This clock, regulated many bodily functions, like secretion of melatonin, a hormone from the pineal gland. Changes in physiology & behaviour are linked to the central clock through changes in the levels of the hormone Melatonin Melatonin - controls sleep- wake cycles, synthesis is active at night time, inhibited during the day. several conditions interfere with normal circadian cycling. Symptoms of Jetlag, lack of appetite, fatigue, insomnia, mild depression. CR controls a number of processes, circadian clock cannot be automatically reset to the new light conditions, may take a few days to become readjusted & entrained. Plants & animals, cycles of seasonal activities, timing of flowering and dormancy. animals, migration or hibernation.
Melanin
A pigment that absorbs UV radiation & gives the skin its color Humans synthesize melanin in specialised skin cells called Melanocytes People from countries receiving a lot of sunlight like Uganda, have more melanin in their skin than people from regions receiving less direct sunlight, like Sweden The presence of Melanin prevents the DNA damage in skin cells that is linked to the development of skin C. Melanin prevents UV radiation from penetrating the skin & destroying the essential B vitamin Folate Melanin filters out damaging UV wavelengths, humans require some ultraviolet radiation to synthesize Vit D, which is critical for normal bone development. People with high melanin levels who live in regions that do not receive abundant sunlight are susceptible to Vit D deficiency, like African living in Sweden In most developed countries, inadequate Vit D intake is rare, coz many foods like milk,yogurt cereals & breads are fortified with Vit D Inuit- native to the arctic, although inhabit a sun-poor environment,have dark skin, because their traditional diet is full of marine life like fish which is naturally high in Vit D
absorption spectrum
A plot of the amount of light a pigment absorbs in relation to the wavelength of light
Action spectrum
A plot of the effectiveness of different wavelengths of light on a biological process is called an AS Because pigments do not absorb all wavelengths of light equally, the effectiveness of light in driving processes that use the absorbed light, like photosynthesis or vision, varies, depending on the wavelength of the light Red and Blue wavelengths of light- more effective at driving photosynthesis than green wavelengths Some photosynthesis still occurs under green light - because photosynthesis involves a number of accessory pigments that can absorb wavelengths of light between the red and blue wavelengths used by chlorophyll
Conjugated System
A region where carbon atoms are covalently bonded with alternating single and double bonds. This bonding arrangement is called CS A common feature of all pigments that is critical for light absorption Results in the delocalization of electrons, none of these electrons are closely associated with a particular atom, which is why they are more available to interact with a photon of light
phytochrome
A type of light receptor (photoreceptor)in plants that mostly absorbs red light and regulates many plant responses, such as seed germination and shade avoidance. Critical for photomorphogenesis - the normal developmental process activated when seedlings are exposed to light. Present in the cytochrome of all plant cells When plant exposed to red light, phytochrome becomes active, initiates a signal transduction pathway that reaches the nucleus In the nucleus, these signals activate hundreds of genes, many of which code for proteins involved in photosynthesis and leaf development
Cataracts
A vision deteriorating disease A change in the lens of the eye making it more opaque The underlying cause is a progressive denaturation of one of the proteins that make up the lens. The increased opaqueness of the lens absorbs certain wavelengths of light, decreasing the transmittance of blue light. Thus to a cataract sufferer, the world appears more yellow
Photons
A wave of light consists of discrete packets of energy called PHOTONS light, described as a wave, but also behaves as a stream of energy particles
How light is absorbed
Absorption of light occurs when the energy of a photon is transferred to an electron of the pigment molecule Electrons occupy discrete energy levels, or excited states, in their orbits around the nucleus of an atom. Before absorbing a photon of light,an electron exists in the ground state. Upon absorption of a photon of light, the energy is transferred to the electron, moving it from the ground state to a higher energy excited state. For a chlorophyll molecule, the electron involved in photon capture can exist in 2 & only 2 excited states. The lower excited state (1), reached by chlorophyll absorbing a photon of red light The higher excited state (2), reached by chlorophyll absorbing a photon of blue light Absorption of blue light excites an electron to a higher energy state than absorption of red light because blue photons contain more energy
Light as a source of Energy
After a photon of light is absorbed, an electron in a pigment molecule is raised to a higher energy excited state. This excited state electron is a source of potential energy that can be used to do work. This potential energy is used in photosynthesic ETC to synthesize energy-rich compounds NADPH (reduced form of NADP) and ATP, which are used to convert CO2 into carbohydrates. Some of the chemical energy is used to synthesize other biological molecules like lipids, proteins & nucleic acids, from simple building blocks found in the environment Energy of a single photon is very small, but millions of photons absorbed each second by the photosynthetic apparatus within the chloroplast of a single C.reinhardtii cell Organisms use light as a source of energy in other processes
using colour as signals
Animals use bright colours to signal that they are distasteful &/or armed & dangerous. To be effective, a signal must be received, so if the signal receiver is blind to colour, the signal is of no use. Eg. other signals of animals, buzz of a bee, odour of a skunk, rattle of a rattlesnake Diversity of colours & patterns of flowers, not designed to please humans but to attract animal pollinators. POLLINATION, movement of pollen from the anthers( male parts) of one flower to the stigma(female parts) of the same or other flowers for fertilization & production of seeds. pollinators, obtain super-rich nectars & protein-rich pollen at flowers Plants that use animals as pollinators must attract correct candidates to ensure pollination & not waste pollen & nectar Flower shape, color, smell, make them more attractive to specific groups of pollinators Pollinators, perceptions of light of different wavelengths, attracted to flowers of specific colours Hummingbirds, red flowers bees, yellow & blue flowers, also perceive UV light, attracted to flowers with UV reflecting pigments.
Diversity of pigments
Chlorophyll a - involved in photosynthesis 11-cis-Retinal - involved in vision Indigo - used to dye jeans their distinctive blue color Phycoerythrobillin - red photosynthetic pigment found in red algae Carmine - scale pigment found in some insects Beta-carotene - an orange accessory photosynthetic pigment
Eyespot
Group of cells that can detect changes in the amount of light in the environment 1 um in diameter located in the chloroplast of a C. reinhardtii cell, close to the Cell membrane located in the chloroplast but does not play a role in photosynthesis Photoreceptors of the eyespot allow the cell to sense light direction and intensity. using a pair of flagella, C.reinhardtii cells can respond to light by swimming towards or away from the light source, a process called PHOTOTAXIS This allows the cell to stay in the optimum light environment to maximize light capture for photosynthesis. Light absorption by the eyespot is linked to the swimming response by a signal transduction pathway, in which light absorption triggers rapid changes in the concentrations of ion, including K+ & Ca, which generate a series of electrical events These, in turn, change the beating pattern of the flagella used for locomotion
Why light?
It is a small portion of the total ES but this small portion is essential to life on Earth These wavelengths, from 400nm to 700nm are the only wavelengths used for photosynthesis, vision, phototaxis, navigation & many other light driven processes. Light is used by organisms bcoz it is the most dominant form of ER reaching Earth's surface. Shorter wavelengths of ER are absorbed by the ozone layer high in the atmosphere, Longer wavelengths than those are absorbed by water vapour & CO² in the atmosphere Another reason- has to do with the energy it contains. Living things are made up of molecules held together by chemical bonds. Radiation of shorter wavelengths than light contains enough energy to destroy these bonds. Absorption of high energy photons wouldn't just excite electrons within a pigment but actually oxidize the molecule producing ions. due to this, shorter wavelengths of ER are often referred to as ionizing radiation Wavelengths longer than those comprising light would not supply enough energy to excite the electrons necessary for photochemistry. Also, longer wavelengths are readily absorbed by water, which is the bulk of all living things.
Ecologic Light pollution
Light bulb, greatest invention that allowed people to carry out pursuits at night that otherwise would not have been possible. But rapid proliferation of artificial lighting that illuminates public buildings, streets and signs has resulted in light pollution, which has transformed night time environment over significant portions of Earth's surface. Presence of artificial light disrupts orientation in nocturnal animals otherwise accustomed to operating in the dark. Eg.newly hatched turtles, emerge from nests & orient themselves towards the ocean because it is brighter than the dark dunes. they head inland and don't survive. 100 & 1000s of migrating birds, don't survive when they collide with lightened buildings & towers
Indirectly damage by light
Light from the sun, harmful to life indirectly because of the UV radiation UV - this is the ER between blue light and x-rays, consists of wavelengths between 200nm to 400nm. Life on Earth - protected from the most damaging form of UV light, UV-C, by the atmosphere's ozone layer. Longer wavelengths of UV radiation, UV-B & UV-C reach the Earth's surface Because of its high energy, UV radiation can randomly ionize the atoms in many types of molecules, like pigments & proteins DNA- structure vulnerable to damage Interaction of UV light with nucleotide bases that make DNA, results in the formation of THYMINE DIMERS, when 2 neighbouring bases become covalently linked. Dimers can change the shape of the double helix structure of DNA & prevent its replication & hinder gene expression. Cells have efficient mechanisms to repair damage to DNA. But Dimer formation can lead to genetic mutations which are harmful. for most organisms, exposure to sunlight & damaging effects of UV radiation is unavoidable. So they use a range of behavioural, physiological & biochemical mechanisms to protect themselves Animals - avoid intense sunlight, shield skin with fur/feathers Naked skin, like humans, rely on producing MELANIN as an imp protective mechanism
Bioluminescence
Many organisms include some bacteria, algae, fungi, insects, squid & fish are bio luminescent, they produce light Chemical energy in the form of ATP excites an electron in a substrate molecule to a higher excited state, and when the electron returns to the ground state, the energy is released as a photon of light. Bioluminescent reactions are very efficient, light bulb 95% energy lost as heat, less than 5% energy in biolumi is given off as heat. this is essential because high heat production would be incompatible with life. Bioluminescent organisms use light to attract a mate, for camouflage, to attract prey or to communicate. Dinoflagellates, unicellular algae, use this as an alarm bell to scare off predators. Bioluminescence is triggered just by the disturbance of water around them. when small fish swim close to dino at night, the burst of light produced by dino lights up the water around the fish, making it clearly visible to it's own predators. defensive behaviour Marine bacteria, use bioluminescence as a type of communication called QUOUM SENSING. Individual bacteria release compounds into their environment, too low to elicit a response from their neighbours. when bacterial populations grows & reaches a threshold, a quorum, where the concentration of compounds is high enough to elicit a physiological response in all members of the population. Response, activates genes that encode for proteins required for biolumi Quorum sensing, basis of milky seas Forest at night, glowing light here and there, called Foxfire. It is produced by bioluminescent fungi growing in rotten wood, probably to attract insects that disperse spores, but some biolumi fungi use wind to disperse spores. in these fungi, the vegetative body produces light not the spore producing structure most bioluminescent organisms, marine and abundant below 800m, depth at which sunlight does not penetrate Bioluminescence not found in land plants
24 he rhythmicity
Many physiological and behavioural phenomena possess 24hr rhythmicity- they vary depending on the time of day. Eg, sleep-wake cycles, body temperature, locomotion, metabolic processes, cell division & behaviours associated with foraging for food & mating
Life in the dark
Nocturnal animals see very well under dim light, moths, fish, bats & frogs Blind mole rat, years of adaptation to life in the dark, natural degeneration of the blind mole's visual system to the point that it is blind. they have small eyes, covered by layers of tissue. but the photoreceptors of the eye remain functional. Since the rats are exposed to brief periods of natural light, the photoreceptors allow entrainment or setting of their biological clock and control of their circadian rhythms. the image forming part of the brain is reduced, the SCN is well developed & receives information from the eyes
Rhodopsin
The basic light-sensing system found universally in all organisms, is the PHOTORECEPTOR The most common photoreceptor in nature is RHODOPSIN, which is not only the basis of vision in animals, but also used by many other organisms like C. reinhardtii, where it serves as the light-sensing unit of the EYESPOT Each rhodopsin molecule consists of a protein called OPSIN, that binds a single pigment molecule called RETINAL. Opsins are membrane proteins that span a membrane multiple times and form a complex in the centre Absorption of a photon of light causes the retinal pigment molecule to change shape, from the 11-cis- retinal to trans- retinal (isomerization) This change triggers alterations to the opsin protein, which in turn, triggers downstream events, including alterations in intracellular ion concentrations and electrical signals. These electrical signals are sent to the visual centres of the brain Rhodopsin, similar to bacteriorhodopsin found in halobacterium & other prokaryotes A light-sensitive pigment found in the rod cells that is formed by retinal and opsin. In humans, capturing of light by the eye, involves about 125 million photoreceptor cells (rods and cones) that line the retina. each photoreceptor contains thousands of individual rhodopsin molecules Most common photoreceptor because it developed very early in the evolution of life vision and smell-different senses but proteins similar to opsin are used on olfaction, meaning specific aspects of opsin proteins are useful for sensory perceptions
single-lens eye
The cameralike eye found in some invertebrates and most vertebrates. Light enters this eye through the transparent cornea, a lens concentrates the light and a layer of photoreceptors at the back of the eye, the retina, records the image
Why is Chlorophyll green?
The color of a pigment is determined by the wavelengths of light it CANNOT absorb Chlorophyll is green because, although it can trap photons of blue light and red light, it cannot absorb photons of green light. because it does not have an energy level matching that of a green photon whereas red and blue photons are captured, green photons are reflected or transmitted, giving chlorophyll and plants its distinctive green color
ocellus, ocelli
a simple eye in many types of invertebrates Consists of about 100 photoreceptor cells lining a cup or pit. Eg. Planarians, in which photoreceptor cells in a cup like depression below the epidermis are connected by bundles of nerves to the cerebral ganglion. Each ocellus is covered on one side by a layer of pigment cells that block most of the light rays coming from the opposite side of the animal Thus, most of the light received by pigment cells enters the ocellus from the side it faces Through integration of information transmitted to the cerebral ganglion from the eyecups, planarians orient themselves so that the amount of light falling on the 2 ocelli is equal and diminishes as they swim This reaction carries them away from the light source, towards darker areas, where the risk of predation is less. Ocelli, occur in a variety of animals, insects, arthropods & molluscs. eye of planaria, not very different from eyespot of C.reinhardtii. in both eye is used to sense light direction and intensity to a light source but little else. Greatest advance in vision, sophisticated eyes that produced an actual image of the lighted environment for distinguishing between objects and shapes. 2 image forming eyes: COMPOUND EYES & SINGLE-LENS EYES
Direct damage by light
although not as energetic as other forms of ER, light is still a form of energy that can directly or indirectly damage biological molecules. All organisms exposed to sunlight, have developed mechanisms to help prevent light induced damage or repair it quickly if damage occurs Eg: Photosynthesis Photosynthetic apparatus- consists of photosystems, pigment-protein complexes that trap the energy of light & convert it to chemical energy. Normal chloroplasts consist of 100s of photosystems, each trapping the energy of about 10000 photons of light each second. Although a photosystem is very efficient at converting light energy into chemical energy, the high energy environment within its core can damage its protein components. Damage to photosystems is unavoidable, rapid repair of damaged photosystems developed early during evolution of life so that the rate of photosynthesis can be maintained even under high light conditions Besides an active repair system, all photosynthetic organisms have CAROTENOIDS, accessory pigments that can protect the photosynthetic apparatus from high light levels by absorbing excess light and safely dissipating the energy as heat. Although carotenoids are not nearly as abundant as chlorophyll, they are absolutely required to protect the photosynthetic apparatus. Plants unable to synthesize carotenoids turn white when exposed to sunlight because their chlorophyll becomes oxidized & its light harvesting capabilities destroyed
Compound Eyes
eyes made of many individual light detectors, each with its own lens Common in arthropods such as insects and crustaceans Each contains 100s to 1000s of ommatidia (omma=eyes) units fitted closely together Each ommatidia has a cornea that directs light into the crystalline cone. The cone focuses light on the photoreceptor cells. A light blocking pigment layer at the sides of the ommatidium prevents light from scattering laterally in the compound eye. From these light signals the brain receives a mosaic image of the world. Even the slightest motion is detected simultaneously by many ommatidia, compound eyes are extraordinarily adept at detecting movements
fundamental property of light
light energy must be captured by the organism
sensing light
may organisms sense the light in their surroundings even though they lack eyes Plants, algae, invertebrates, some prokaryotes
Electromagnetic radiation
self-propagating waves which consist of both electrical and magnetic waves, which are oriented at 90° to each other Energy from the Sun, which travels at the speed of light, reaches Earth in about 8 mins Electromagnetic radiation moves in the form of 2 waves: 1 electrical & 1 magnetic, which are oriented at 90° to each other Scientists distinguish ER by its WAVELENGTH - the distance between 2 successive peaks Range- less than 1 picometer (10‐¹² m) for cosmic rays to more than a kilometre (10⁶ m)for radio waves
camouflage
the act of concealing the identity of something by modifying its appearance Works when 1 animal fails to distinguish another from the background. pattern & behaviour play central roles in camouflage.
PHOTONS 2
unlike atoms, have no mass, but each contains a precise amount of energy Amount of energy in a photon is inversely related to its wavelength Blue light - shorter wavelength, photons have higher energy Red light - longer wavelength, photons have less energy
Light in aquatic habitats
water attenuates light, no light reaches below about 150m water absorbs longer wavelengths of light more effectively than shorter wavelengths Below 30m, light is monochromatic, consists only of blue wavelengths Red algae, survive at greater depth in the ocean than many other photosynthetic organisms because they have PHYTOERYTHRIN, an accessory photosynthetic pigment not found in land plants. Phytoerythrin absorbs blue wavelengths of light, giving red algae their distinctive color Fish in shallow marine water, brilliantly coloured, species living in the deep are silver and black bodied, making them less conspicuous.
