Light and Life: chapter 1
LIGHT IN CONTACT WITH MATTER………………………..4
LIGHT AND LIFE………………………………………………..……5
ROLE OF LIGHT IN ECOLOGY AND BEHAVIOUR…….7
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)
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
(With Dr. Gadsgen)
*Italic text underlines material from Dr. Gadsgen’s lectures
LIGHT AND LIFE
-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
-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 macromolecules3D 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
Structure in position to
hence, make or break
*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
ATP: the magic molecule
Phosphoester: if carbon replaced phosphate, bond would become an ester
Chlamydonasprotocoa (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
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 lightaffects 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
Blue and red wavelengths have higher absorbency than green wavelengths: why? Because of
Retinual is not a protein: it absorbs light.: LIGHTStructure changeallows Protons to cross
Diffusion: The action of spreading the light from a light source evenly so as to reduce glare and
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
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
-When photoreceptor comes into contact with light, it changes structure
5 - Protein undergoes some conformational change
- Signal transduction cascade¸
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 nervebrain Superchiasmic
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
Camera eyes are image forming and can
DNA sequence changemutationsmost
mutations are badrarely, 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
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
Light has effects on melatonin production: melatonin affects sleep
Retinol transforms chromoform-absorbs photons
Opsinscis formvision, 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
-Using colour as signals
-Light in aquatic environments
7 CIRCADIAN RHYTHMS:
24 hour cycle that influences sleep patterns
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.
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
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
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
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
In spectrometer [email protected]
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 copiedDNA polymerase makes new DNA called Nascent Strandmakes a 5’
to 3’ directionmutationinherited if not repaired
*If a mutation occurs in the RNA it is not a real mutation as it cannot be inherited or
Drugs work by blocking replication, which can allow the cells to repair themselves before being
Triptophane makes melatonin These three amino acids are all related to melatonin
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 (askascientist.org).
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
H1N2common flu H1N1adapted 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 virusbig step in virus evolution, isn’t
What is normal?
“positive” or “silent”
m- leads to better
fitness, which leads to
Doesn’t affect you
ability to live in
Nother 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
-Respond to stimuli
-Growth and development
*Homeostasis: internal system that regulates and balances pH, body temperature, etc.
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