QUIZ 1 Flashcards
What is the difference between Rayleigh and Mie scattering efficiencies, specifically their relationships between scattering efficiency and wavelength?
In Rayleigh scattering, efficiency is related inversely to the fourth power of wavelength
In Mie scattering, efficiency is not strongly dependent on wavelength
Rayleigh scattering efficiency is related to the inverse of wavelength to the fourth power
Mie scattering efficiency is not strongly related to wavelength
How does this difference rationalize the colour of the sky and the clouds?
Clouds are water vapour particles which are much larger than the small molecules making up the air. This means clouds are a result of mie scattering -> all wavelengths scattered equally efficiently (white/grey)
The general air molecules in the sky are a result of Rayleigh scattering which scatters smaller wavelengths most efficiently -> blue sky
What optical behaviour is responsible for the difference between the blue ish colour of skim milk compared to the pure white colour of whole milk?
Rayleigh and Mie scattering.
Rayleigh scattering occurs in skim milk because there are no lipid (larger) molecules and Rayleigh scattering is most efficient with small wavelengths like blue. Mie scattering occurs in whole milk because of the larger lipid molecules, resulting in scattering of all wavelengths equally and a white colour.
What is the biological optical window? (Used for diagnostics)
700-1000nm is the biological optical window
When removing phosphates from ATP, how many phosphates should be removed for maximum energy efficiency?
Only 1 phosphate should be removed ATP -> ADP +Pi (-30.5 kJ/mol)
Because the relationship is not linear as removing 2 phosphates does NOT release double the energy (-45.6kJ/mol)
Where does photosynthesis take place?
Photosynthesis occurs in the thylakoid membrane
How do chlorophylls a and b differ?
Chlorophyll b has the addition of a double bonded O which changes its absorption spectrum.
The path of a signal from reception to reaction: What steps follow the Reception step?
1) reception
2) transduction
3) conduction
4) analysis and interpretation
5) feedback
In biological sensors, the stimulus is converted to an electrical impulse during which step of a path of a signal?
Step 2) transduction: the stimulus is converted to an electrical impulse
In biological sensors, the electrical impulse is carried to the brain through the nervous system via an AP during which step of the path of a signal?
Step 3) Conduction
What are the three different types of biological sensors?
Light, chemical, mechanical
The auditory system relies on what type of biological sensor?
The auditory system, where sound waves (pressure changes) make the ear drum vibrate, relies on mechanical biological sensors
What are the 5 devices required for an artificial biosensor?
Artifical biosensor
1) biorecognition element
2) transducer
3) amplifier
4) signal converter
5) recording device
In an artificial biosensor what is the role of the transducer?
The transducer converts the stimulus into an E signal
In an artificial biosensor, what is the role of the amplifier?
The amplifier boosts the voltage of the signal
In an artificial biosensor, what is the role of the signal converter? why?
The signal converter transforms the electrical signal arriving from the transducer from analog to digital so it can be processed by a computer
In the Hodgkin Huxley Model, what do the capacitor, resistors, batteries, and current source each represent?
Capacitor represents the lipid bilayer
Resistors represent the voltage-gated ion channels
Batteries represent the electrochemical gradients
Current source represents the active pumps
What experimental technique is used to study the dynamics of ion channels in the membrane?
The patch clamp technique is used, it can study individual ion channels of a cell
Light intensity and colour vision are handled by different photoreceptor cells. Which photoreceptor cells are responsible for which?
Cone photoreceptor cells handle colour vision
Rod photoreceptor cells handle light intensity
Cone photoreceptors handle colour vision. How can cones explain how various degrees of colour blindness exist?
Various degrees of colour blindness can be explained because 3 different cone types are responsible for the visible light spectra.
Ex: one kind of colour vision deficiency is also called dichromacy because one of your 3 cones is missing or malfuctioning. The colours someone with dichromacy can see depends on which cones are missing or malfunctioning.
What is the difference between ospins and retinal?
Opsins refer to all and any light-sensitive proteins in the photoreceptor cell, whereas retinal is one specific opsin protein
What is the interaction between retinal and light that supports the function of the visual system.
Retinal absorbs incoming light and transforms into an activated version of itself. This ultimately results (*) in the perception of light or images by the brain
this is photoisomerization because light triggers a change in molecular configuration
*from wikipedia lol just for fun
Retinal catches a photon of the correct wavelength -> retinal straightens out and pushes against an opsin protein in the retina -> triggers a chemical signaling cascade -> results in the perception of light or images by the brain
How does the light detected by photoreceptors get converted to electrical impulses, to then be sent to the brain? What is this process called?
Phototransduction is the conversion process which is a result of membrane depolarization and multiple specialized proteins, including GTP and GDP
Channelrhodopsins are light-gated ion channels. What molecules do they contain to allow them to be light-gated?
Channelrhodopsins contain a chromophore located in retinal which responds to specific wavelengths
What is optogenetics?
Optogenetics is a field that uses genetic engineering of ion channel proteins to trigger membrane potential changes (and, therefore, information transfer) from light input.
- from google lol
can investigate how the neurons work together, by using light to turn some neurons on and record the response of other neurons
this is useful for understanding how and when the neurons interact with each toher
What are the three ways to express opsins in neurons?
Virus transduction, transfection and transgenic animal lines
Why would we want to express opsins in neurons?
In order to control membrane potentials with light, opsins need to be expressed in neurons
- from google lol
can investigate how the neurons work together, by using light to turn some neurons on and record the response of other neurons
this is useful for understanding how and when the neurons interact with each toher
What technique can be used to open the cell membrane, allowing the insertion of genetic material?
Electroporation uses an electric field to temporarily render the membrane porous*
*from thermofisher scientific for fun
Host cells and selected molecules are suspended in a conductive solution and an electric circuit is closed around the mix. An electric pulse of a few microseconds is discharged through the cell suspension which disturbs the bilayer, forming temporary pores. The E potential rises which allows charged molecules (DNA) to be driven across the membrane
What is the difference between the knockout mouse and the chimeric mouse?
Knockout: In the embryonic stage of growth, modified genetic material is introduced to embryonic stem cells. As a result, the knocked-out genetic material will be missing across all tissues.
Chimeric: Mice hybrids, carrying two different genomes(one modified), are bred together until a mouse homozygous for the GMO genetically material will be created naturally
In genetically modified organisms, how does light reach the modified neurons?
Small holes are drilled through the skull of the organism, and optical fibers carry light to the target region
What are the benefits of artificial photosynthesis?
Artificial photosynthesis is a
carbon-neutral,
sustainable method
for generating energy by splitting water to form molecular hydrogen.
Water splitting like this can be achieved by a proton-coupled multi-electron transfer process, allowing for net energy to be produced.
By the Huygens-Fresnel Principle,
When light interacts with a material at an interface, points of interaction will be sources for new circular waves these waves will then interact with eachother, creating a wave front
By Fermat’s principle,
Light will always take the path requiring the shortest time when traveling between two points
What determines if a photon is scattered or absorbed?
“If a photon does not strike molecules in the ““correct way””, the photon will be scattered instead of absorbed”
A mirror is an example of when reflection is diffuse or specular ?
A mirror is an example of when reflection is specular, where the angle of incident light is equal to the angle of reflected light
What causes reflection to be diffuse?
Diffuse means that light rays will be reflected in multiple different directions due to imperfections in the surface
Reflected light A has a higher intensity than reflected light B but both originate from incident light of the same intensity.
Which light has a smaller angle of incidence?
Generally, larger incident angles translate to lesser light intensities so reflected light A has a smaller angle of incidence
What are the four main behaviours that allow light to interact with matter?
reflection, absorption, emission, and scattering
A photon strikes an object and the energy of the scattered photon does not match that of the incident photon. Which kind of scattering is it?
Because of the change in energy between the incident and the scattered photons, this scattering must be inelastic so it is raman scattering
What is raman scattering?
Raman scattering is inelastic scattering which results in a polarizaility change in the molecules struck by light
What is the difference between Mie and Rayleigh scattering?
Mie and Rayleigh scattering are both elastic, but Mie scattering applies to objects similar in size to the light’s wavelength, whereas Rayleigh scattering applies to objects smaller in size to the light’s wavelength
Which type of scattering can rationalize the blue colour of the sky?
Rayleigh scattering, the elastic scattering on objects smaller than the wavelength of light, because atmospheric particles are smaller than the wavelength of light
Also, they scatter the shortest wavelengths of light (in the visible spectrum this is blue light) the most which results in the blue colour
Which kind(s) of scattering is elastic?
Both Rayleigh and Mie scattering are elastic
What is scattering?
Scattering in general is the deflection and/or diffusion of light
Do glowsticks use phosphorescence or fluorescence?
Glowsticks are able to glow for hours,
so they use phosphorescence which has lifetimes in the order of hours
Does phosphorescence or fluorescence have longer lifetimes?
Phosphorescence have longer lifetimes which are on the order of hours whereas, fluorescence lifetimes are on the order of nanoseconds
What is phosphorescence?
Phosphorescence is the absorption and subsequent emission of light which occurs for far longer
Fluorophore A’s light emission lasts for 10 ns while Fluorophore B emits light for 20ns
Which fluorophore has a higher fluorescence lifetime?
Fluorophore B has a longer light emission time therefore its fluorescence lifetime is larger
What is the fluorescence lifetime?
The fluorescence lifetime is the measure of how long the molecule in question will remain in the excited state
Why is the quantum yield always less than 1?
The quantum yield is always less than 1 to reflect that some energy is always lost to heat
What is the quantum yield?
The quantum yield of a compound fluorescence is the ratio of the number of emitted photons over the number of absorbed photons
What is stokes shift?
Stokes shift refers to the difference between the absorption wavelength and the emission wavelength during fluorescence
What is the difference between endogenous and exogenous fluorophores?
Endogenous fluorophores are naturally occuring within cells
Exogenous fluorophores are introduced to cells, typically for experimental purposes like tagging
What are fluorophores?
Fluorophores are molecules that fluoresce
What is fluorescence?
Fluorescence is the absorption of light quickly followed by its emission
What kind of luminescence is bioluminescence?
Bioluminescence is a from of chemiluminescence
What happens to the E that decays non radiatively?
Energy that decays non radiatively is released as heat due to atoms vibrating
What values would you need to know to calculate total rate of decay?
Total rate of decay = radiative decay rate + nonradiative decay rate
How can light be generated? (3)
Light can be emitted by heat sources, through luminescence, and radioactivity
What kind of objects emits blackbody radiation?
All objects with temperature above absolute 0K
How are lasers different from other light sources? (4)
Monochromatic (single wavelength)
coherent
directional
polarized
What does it mean for light to be polarized?
Unpolarized light has their pairs of electric and magnetic waves propagating in a variety of planes.
Polarized light means their pairs of electric and magnetic waves propagate in a single specific set of perpendicular planes (one plane for E one plane for the corresponding perpendicular M waves)
What is the lorentz force?
The lorentz force is the force that results from particle movement in an EM field
F(lorentz) = qE + qv (B)
What is permittivity?
Permittivity: The capacitance that is encountered when forming an electric field in a medium
What is permeability?
Permeability: Ability to support magnetic fields
Shrimp are able to create light by quickly opening their claws, creating an air bubble which expands and collapses, resulting in the emission of light.
What is the name of the mechanism by which shrimp generate light with their claws?
Mechanoluminescence, because the quickly expanding air bubble collapses due to pressure resulting in an ionization then emission of light
What characteristic of lasers allow them to create regions of high E energy density?
Laser’s unidirectionality allows them to focus light, focus energy, creating regions of high energy density
What kind of emission is used to achieve coherence (ex: coherence of a laser)?
Stimulated emission is used to create the coherent light emitted by a laser
How is directionality acheived?
Mirrors are used to force light into a single direction
Which component of the eye controls the amount of light coming in?
The pupil aperture
What is the optical function of the cornea?
The specific shape of the cornea refracts and focuses light -> it is the main focusing power of the eye
What is the advantage of having a pinhole aperture?
A pinhole has no focusing issue, regardless of distance everything in the field of vision is in focus
What is the drawback of a pinhole?
A lot of light is required
What are the conditions required for total internal reflection? (Pair of media)
Total internal reflection can only happen when light travels from a medium with high refractive index to a medium with lower refractive index
Is decay a natural or stimulated process?
Like absorption, decay can be natural or simulated, a catalyst like photon triggers the emission of a 2nd photon from the atom
How do lenses focus light on a specific point or scatter light away from a specific point? (How do they manipulate the waves?)
Lenses convert planar waves into circular waves to focus or scatter light
Can filters focus or reflect light?
No filters only control the intensity of light as well as its spectral characteristics
What force is responsible for many phenomena, like binding of electrons to nuclei and intermolecular interactions?
The Lorentz force: the force exerted on a charged particle moving in an electric and magnetic field
By Gauss’s Law (electric charges)…
Electric fields are generated by single charges and diverge
By Gauss’s Law (magnetism)…
No “magnetic charge” exists
Magnetic fields are generated by dipoles and do not originate in a single point
By Faraday’s Law of Induction…
A spatially varying electric field is accompanied by a temporary varying magnetic field
By Ampere’s Law…
Magnetic fields can be generated in two ways
by electric currents and/or
by changing electric fields
When burning a hole through a piece of paper, using a magnifying glass and sunlight, how far away must the paper be placed from the lens?
The paper must be placed at a distance equal to its focal length
The paper will begin burning at the focal point
Light travels in a straight line through medium 1 and light travels in a z-like path through medium 2.
What does this tell you about medium 1 and medium 2?
Medium 1 is a uniform substance
Medium 2 is a non uniform substance
Object 1 results in specular reflection and object 2 results in diffuse reflection.
What does this tell you about objects 1 and 2?
Object 1 must have a smooth shiny surface
object 2 must have a rough textured surface
What is the difference between a real or a virtual image?
A virtual image is formed when light rays diverge after reflection
A real image is formed when light rays converge after reflection
Do mirrors produce real or virtual images?
Plane mirrors and convex mirrors produce only virtual images
Concave mirrors can produce both real and virtual images
What is the difference between a real and a virtual image?
Virtual images appear behind mirror, light rays do not pass through it and it cannot be projected
Real images appear in front of mirror, light waves pass through it and it can be projected
What is transmittance?
Transmittance measures how much light is able to pass through a material
An action potential from node to node is also called what?
A saltatory conduction
Which ion channels are responsible for allowing hyperpolarization and depolarization?
Voltage-gated ion channels
Do APs propagate in myelinated or in non-myelinated axons?
APs are propagated in both myelinated and non-myelinated axons
Myelin allows for faster propogation
Empty card
:)
Name the differences/similarities between natural and artificial photosynthesis
Natural:
- Makes oxygen, ATP, Glucose
- water is electron donor
- NADP+ is electron acceptor
- Has photo systems and reaction centres
- Has Light independent rxn
- Occurs in thylakoid membrane and stroma
- electron transport chain
Artificial:
- makes oxygen and hydrogen
- electron donor is water
- electron acceptor is 2H+
- has chromophores (dye or semi-conductor)
- water splitting occurs on silicon platform with catalysts
- no light indep reaction
- multi e-transfer process
Consider a set of 3 charges (A, B, C)
Using Coulomb’s law
F(A & B) > 0
F(A & C) < 0
If A is a negative charge, what are the signs of charges B and C?
When F is negative, the charges attract and vice versa
A -
B -
C +
Consider a set of 3 charges (A, B, C)
Using Coulomb’s law
F(A & B) > 0
F(A & C) < 0
Which force attracts and which force repels?
F(A & B) is positive so the charges repel because the charges are of the same sign
F(A & C) is negative, so the charges attract because the charges are opposite signs
What is the Van der Waals radius?
The Van der Waals radius is reached when potential is zero
it is the perfect distance between particles to avoid attraction and repulsion
When two non bonding particles are an infinite distance apart, what is their bonding potential energy?
The possibility of them coming together is so minimal, so their bonding potential energy is considered 0
Two bound particles are pressed together past their equilibrium distance, what is their bonding potential energy?
Repulsion begins to occur, as the distance of separation decreases, bonding potential energy increases to infinity
Which intramolecular interaction occurs between cysteine amino acids in protein chains to strengthen and stabilize tertiary structures?
Disulfide bonding
What conditions and forces cause surface tension?
Surface tension is the result of cohesive forces between molecules at an interface
A newborn with respiratory distress syndrome has abnormalities in the composition of a compound in the lung. This leads to too much surface tension in the lung which causes their alveoli to collapse after exhalation. What is the name of the dysfunctional compound?
Surfactant is dysfunctional
surfactants are compounds which lower surface tension by distrupting intermolecular forces at the interface
Which forces are responsible for capillary action?
Cohesion and adhesion forces
What is the difference between cohesion and adhesion?
Cohesion: the binding of liquid molecules to eachother
Adhesion: the binding of liquid molecules to a surface
Hydrophobicity is a result of what?
Hydrophobicity is a result of entropy
Since hydrophobicity results in non-polar groups aggregating, how does this agree with the theory of entropy? (non-polar groups seem to “self-organize” which “contradicts” the universal drive towards disorder)
When non-polar molecules are all separate they each have an organized cage structure of water molecules to envelop them.
When non-polar molecules aggregate, this disturbs the unique water cages, which makes the water more disorganized, increasing the overall entropy of the universe.
Explain the ring of coffee that forms after you spill a bit of coffee around the base of a cup, using thermodynamics
Surface tension and connective forces drive the effect
When the outer layer evaporates, a slight T differential is created between the outside and inside of the ring
Convection occurs within the ring, pushing smaller particles out towards the edge of the ring, larger stay in the middle
So the outside of the ring looks darker due to being highly concentrated in small particles by the edge
The coffee cup ring effect can be used as inspiration for developing what methods?
Methods for concentration and methods for sorting mixture components
In networks, what is the difference between edges and nodes?
Networks are combinations of various nodes, representing elements, liked together via edges, representing relationships between elements in the network
What is an example of a network?
Human disease network
Interactomes (protein-protein interactions)
What filter changes the intensity of light but not the wavelength?
Neutral density filters
What kind of filters only allow a specific range or band of wavelengths to pass through
Bandpass filters
Which filters allow only a long wavelength to pass?
Long-pass edge filters
Which filters only allow a very small range of wavelengths to pass?
Dichroic filters
You want to use a filter to let all wavelengths through except those from 750nm-780nm. Which filter do you choose to use?
Notch filter
In photography, to make light more ambient which filter is used?
Diffusers
What is the benefit of the Fresnel lense?
The fresnel lens operates like a convex lens, imitating the same slopes and curvature of glass but with less material
How is light detected by photoreceptor cells then converted to electrical impulses which are then sent to the brain?
Phototransduction is the process where by membrane depolarization and specialized proteins such as GTP and GDP, light detected by photoreceptors is converted to electrical impulses which are then sent to the brain
Which energy carriers are used in photosynthesis?
NADPH and ATP are the energy carriers used in photosynthesis to transfer energy from location to location
What mechanism of the AP results in the unidirectionality of APs in neurons?
The refractory period of the previous neuron prevents the action potential from going backwards
MS is a disease where action potentials travel at least one order of magnitude slower in certain neurons compared to the same neurons in healthy individuals. What components of neurons are MS patients lacking which result in these slower speeds of propagation?
MS patients have neurons that can lack myelination
What are the two major benefits of having synapses when transmitting action potentials?
Prevent signals from traveling backwards and
signal amplification
How do synapses maintain the strength of APs?
The signal is completely regenerated to full strength after being passed to the next neuron due to the neurotransmitter synapse mechanisms to transmit action potentials
How do synapses prevent signals from traveling backwards?
There are no receptors for neurotransmitters at the presynaptic region at the end of the neuron
