fSeptember 16, 2013
Biology Textbook Notes
Ch.1: Light and Life
•Light is the portion of the electromagnetic spectrum that humans can detect with
•Light has no mass.
•Light is composed of a stream of energy particles called photons.
•Light has properties of both a wave and stream of photons- particle-wave duality.
•The longer the wavelength= the lower the energy of the photons it contains.
•When photon hits object it can be reflected, transmitted through the object or
•To be used as a source of energy/information by an organism, absorption must
•Absorption of light occurs when energy of the photon is transferred to an electron
within a molecule- exciting the electron.
•Pigments are molecules that are efficient at absorbing photons.
•All pigments share a critical feature: a region where carbon atoms are
covalently bonded to each other with alternating single and double bonds
•A pigments colour is the result of the photons that it does not absorb.
•The potential energy of excited electrons is used in photosynthetic electron
transport to synthesize NADPH and ATP.
•NADHP and ATP are consumed in the Calvin cycle to convert carbon dioxide into
•Cellular respiration breaks down carbs trapping the released energy as ATP.
•Halobacterium- contains a pigment-protein complex called bacteriorhodopsin,
which functions as a light-driven photo pump.
• Captures photons of light that supply the energy needed to pump protons out of
•Resulting H + concentration represents a source of potential energy that is used by
ATP synthase to generate ATP from ADP and inorganic phosphate.
Rhodopsin, the universal photoreceptor
•Photoreceptor: basic light sensing system.
•Rhodopsin is the most common photoreceptor in animals, but also present in other
organisms like C.reinhardtii, where it serves as the light-sensing unit of the
•Rhodopsin molecule consists of a protein called opsin that binds a single pigment
molecule called retinal.
•Rhodopsin is structurally similar and evolutionary related to the bacteriorrhodpsin
found in Halobacterium.
•Absorption of a photon of light causes the retinal pigment molecule to change
•Electrical signals are sent to the visual centers of the brain.
•In humans the photoreceptor cells are called cones and rods.
•The eyespot is a light sensitive structure found within the chloroplast of the cell.
•The eyespot is composed of two layers r carotenoid-rich lipid globules that play a
role in focusing and directing incoming light toward the photoreceptors.
•The eyespot does not play a role in photosynthesis.
•The photoreceptors of the eyespot allow the cell to sense light direction and
•Using a pair of flagella, C.reinhardtii cells can respond to light by swimming
toward or away from a light source process called phototaxis.
•Light absorption by the eyespot is linked to the swimming response by a signal
•In plants, a photoreceptor called phytochrome sense the light environment and is
critical for photomorphogensis- the normal developmental process activated when
seedlings are exposed to light,
•Phytochrome is present in the cytosol.
•The process of vision requires an eye and a brain.
•The simplest eye is the ocellus- found in insects, arthropods and mollusks.
•Image forming eyes are found in two distinctly different types:
•Common in arthropods (insects/crustaceans).
•Built by hundreds of individual units called ommatidia.
•Found in some invertebrates and all vertebrates including humans.
•Light enters through the transparent cornea; a lens concentrates the light and
focuses onto a layer of photoreceptor cells at the back of the eye, the retina.
•The photoreceptor cells of the retina send signals to the brain.
•Pax6 is the master control gene that is almost universally employed for eye
formation in animals.
The uniqueness of light
•Visible light is a small part of the electromagnetic spectrum (400-700 nm).
•Shorter wavelengths are absorbed by the ozone; wavelengths longer than those in
the visible spectrum are absorbed by water vapor and CO2 in the atmosphere.
•Photons of light can damage biological molecules.
•Photoreceptor cells that line the retina can be damaged by exposure to bright
light photo-oxidative damage.
•Unlike eyes, photosynthetic apparatus of plants and algae is exposed to full
sunlight for hours and is susceptible to photo oxidative damage.
•Damage to the photosynthetic apparatus is unavoidable so a mechanism of
efficient repair must have developed early during evolution.
•UV light has shorter wavelengths that visible light so the energy of the photons of
UV light is greater and more damaging.
•X-rays, gamma rays, and UV rays are classified as ionizing radiation.
• Interaction of UV light with nucleotide bases that make up DNA can result in the
formation of dimers- can cause mutations.
•Melanin is a pigment that strongly absorbs UV light.
•The specific wavelengths of radiation that a pigment can absorb can be
determined by a spectrophotometer.
•Humans require some UV rays to synthesis vitamin D.
•Diurnal phenomena governed by our biological clock.
•Presence of biological clocks enhances an organism’s ability to survive under
ever-changing environments by giving them the ability to anticipate of predict
when a change will occur.
•Photoperiod= day length.
•Changes in photoperiod provoke changes in the colour of fur, trigger migration
•Peripheral clocks are set by the body’s central biological clock that is found in a
small part of the brain called the suprachiasmatic nucleus.
•The lives of nocturnal animals have been disrupted by light pollution (street
•Light sets the ‘biological clock’ but circadian rhythms aren’t a direct result of
changes in the light environment.
Ch.2 The Cell: An Overview
•1820’s: improvements in microscopes brought cells into sharper focus.
•Robert Brown, an English botanist, noticed a spherical body inside some cells- he
called it a nucleus.
•1828: Matthias Schleiden speculated that the nucleus had something to do with
the development of a cell.
•Theodore Schwann- expanded Schleiden’s idea to propose that all animals and
plants consist of cells that contain a nucleus.
•Rudolf Virchow- proposed that cells arise only from pre-existing cells by a
process of division.
1. All organisms are composed of one or more cells.
2. The cell is the basic structural and functional unit of all living organisms.