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BIOL 1500 Study Guide - Circadian Clock, Accessory Pigment, Electromagnetic Spectrum


Department
Biology
Course Code
BIOL 1500
Professor
Tamara Kelly

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September 7th 2012
Cathy Nguyen=)
Astrobiology
Light
- the portion of the electromagnetic spectrum that humans can detect with their eyes
- categorized as a wave (stream of energy particles)
- these particles are categorized as photons (visible light particle)
- photons have no energy or mass but have precise amount of energy
Ex. Blue light has a shorter wavelength = less photons = less energy than... red light
Ex. Sunburn = human response to light, shows some physical manifestication on you to know that
these particles exist
Ex. Radiowaves = hearing noise is a direct result that it exists
Photoreceptor: a basic light-sensing protein system invovled in sensing and responding to light
(Contains a protein + pigment, the pigment absorbs light photon while the protein undergoes
conformational change)
Eyespot: a heavily pigmented region in certain one-celled organisms that function as a light sensor.
Detects both direction & intensity of light
Interactions with Matter
1. Reflect: bounces off and sent to another direction (occurs b/c frequencies of light waves don't match
with the natural frequencies of vibration of the object, same with transmission)
2. Transmitted: passes through with no interaction
3. Absorbed: most useful for biological, can only use a photon when absorbed (ex. cup of water, can only
be beneficial when we drink it)
Pigments
- a molecule that can absorb photons of light (they differ by different wavelengths each can absorb,
depending on its structure)
- its colour is the colour that was not absorbed, but reflected off
- made from double/single bonding arrangement called conjugated system
Ex. Chlorophyll
Rhodopsin
- a photoreceptor found universally in all organisms
- technically, a pigment in the retina that allows the eye to see in dim light
- made of a protein called opsin, that binds to a single pigment molecule called retinal
In light: A photon is absorbed causing the retinal molecule to under go conformational change, which
results in a whole bunch of other reactions that create electrical signals that are sent to the brain.
Enzymes cause it to reset to original shape (conformational change).

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Light as a Source of Energy
- when a photon of light is absorbed, an electron within the pigment molecule is raised to an excited
state, which is a source of potential energy that can be put to work. This potential energy can be used in
photosynthesis (electron transport chain to synthesize NADPH), when then create ATP>C02>CARBS.
- some of the chemical energy is also used to synthesize other molecules like lipids, proteins, nucleic
acids
Sensing Light without Eyes
- plants, invertebrates, & some prokaryotes don't have eyes but can sense light
Ex. C. reinhardtii: its eyespot is located within the chloroplast in a region closely associated to the cell
membrane. Although it is in the chloroplast, the eyespot does not play a role in photosynthesis but
rather the photoreceptors of the eyespot allow the cell to sense light direction and intensity.
(phototaxis)
- in plants, a different receptor called the phytochrome senses the light environment and is critical for
photomorphogenesis (development process when seedlings are exposed to light).
Phototaxis (+/-): the ability of organisms to move directionally in response to a light source (maximizes
light capture for photosynthesis).
The Eye (the organ animals use to sense light)
- requires a brain/simple nervous system to interpret signals sent from the eye. The eye&brain are
thought to be co-evolved b/c detailed visual processing occurs in the brain rather than the eye. We
essentially "see" with our brain and not our eyes.
Ex. Planarians: ocellus (plural ocelli) is the simplest eye consisting of up to 100 photoreceptors lining in a
cup/pit under the skin. Each ocellus is covered by a layer of pigment cells that block most of the light
rays arriving from the opposite side of the animal. Resulting in most of the light recieved by the pigment
cells to enter from the side it's facing. This way, planarians orient themselves so that the amount of light
falling on the two ocelli is equal and deminishes as they swim. This reaction carries them directly away
from the source of light and toward darker areas.
Imaging-forming eyes
Compound Eyes: common in insects and crustaceans, containing thousands of ommatidia (omma = eye)
units fitted closely together. Each ommatidium samples a small part of the visual field as light enters.
Signals from the photoreceptor cells go to the brain creating a mosaic image of the world. Even the
slightest motion is detected.
Single-lens Eyes: for most veterbrates, light enters the ee through a transparent cornea, a lens
concentrates the light, and a layer of photoreceptors at the back of the eye (retina) records the image.
Evolution of the Eye
- scientists believe that about 2000 small improvements over time from a patch of light-sensitive cells,
gradually yielded a camera-type eye in less than 1/2 a million years.
1) Region of photosensitive cells (just an eyespot, ex. Euglena)

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2) Depressed/folded area allows limited directional sensitivity (eyecup, ex. Dugesia/Planarians)
3) "Pinhole" eye allows finer directional sensitivity and limited imaging (ex. Nautilus)
4) Transparent humour develops in enclosed chamber
5) Distinct lens develop (Primitive lens, ex. Box Jellyfish)
6) Iris and seperate cornea develop
- looking at closely related organisms & how their eyes differ in relation to their environment.
Ex. Limpet - simple layer of photosensitive cells
Slit-shell Snail - simple layer of photosensitive cells curved in eyecup
Nautilus - pinhole camera eye
Squid - advanced camera eye
September 10th 2012
Role of Light in Ecology & Behavior
Light can Damage Biological Molecules: Direct Effects
- light is a small portion of the electromagnetic spectrum et is essential to life on Earth. This is b/c it is
teh most dominant form that reaches the surface. Shorter wavelengths are absorbed by the ozone layer
high in the atmosphere whereas longer ones are absorbed by water vapour and CO2 in the atmosphere.
- also b/c radiation of shorter wavelengths has high enough energy to destroy bonds of living things. It
wouldn't just excite electrons but would oxidize the molecule producing ions (ionizing radiation).
- wavelengths that are longer don't supply enough energy to excite electrons for photochemistry.
Longer wavelengths are also readily absorbed by water (the bulk of living things).
- Light is still damaging, but all organisms that are exposed to light have developed mechanisms to help
prevent damage/repair quickly if damage does occur.
Ex. Photosynthesis: composed of photosystems (pigment-protein complexes) that trap photons and
convert it to chemical energy. Although very efficient, the high-energy environment does cause damage
to the protein complexes. Under high light conditions, carotenoids (accessory pigments) protect the
photosynthetic apparatus from high light levels by absorbing exess light and dissipating the energy as
heat.
Light can Damage Biological Molecules: Indirect Effects
- harmful indirectly b/c of UV rays (ultraviolet radiation). Life on Earth is protected by the most
damaging, UV-C by the ozone layer, however UV-A and UV-B can still reach the surface. B/c of its high
energy, it can randomly ionize atoms in pigment molecules and proteins.
- DNA is very vulnerable to UV damage b/c of its structure, resulting in the formation of a "dimer" when
two neighboring bases become linked. This changes the shape of the double-helix and prevents
replication, hindering gene expression (genetic mutation).
Ex. Animals avoid sunlight by shielding skin with fur/feathers, whereas humans rely on melanin.
Melanin: pigment that absorbs UV radiation, preventing it from penetrating the skin and destroying the
essential B vitamin folate.
Absorption Spectrum: plot of the amount of light a pigment absorbs in relation to the wavelength of
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