BIO OUTCOMES MIDTERM 1
Characteristics of Chlamydomonas that make it a useful model system
Attributes of both plant and animal cells
Good for looking at light energy and information
Model system for photosynthesis, genetics, cell bio
Reproduces sexually and asexually
Easy to create mutants and effects of mutants are clearly seen
Haploid and relatively simple genome
Prokaryote and eukaryote genes in same cell (Nucleus and chloroplasts)
Relatedness of Chlamydomonas to plants and animals
Classified as protist, in chain leading to plants but is not a plant
Eukaryote, shares similarities to plants and animals
Phototransduction from Eyespot to Flagella
Photon hits eyespot, channel rhodopsin changes conformation, membrane becomes depolarized,
creating action potential, action potential travels down to flagella, channel rhodopsin closes and cell
membrane is repolarized, flagella takes action potential and performs photaxis
Advantages to Chlamydomonas in being phototactic
Decreases the chance of producing excess energy by moving away from light
Increases energy production efficiency by moving towards light when needed
Distinctions between primitive, complex, simple.
Primitive: genetically old
Complex: Many different and connected parts
Simple: Basic or uncomplicated
oEyespot is not more primitive than eye but is more simpler
Reasons why Chlamydomonas might move towards a light source.
Increase rate of photosynthesis
Reasons why Chlamydomonas might move away from a light source.
Too much light absorption could result in formation of ROS, resulting in harmful mutations
Has enough energy already, doesn’t need to spend more time doing photosynthesis
Light controls sexual activity; chalmy is sexually active
Possible mutations that could cause a Chlamydomonas cell not to be phototactic.
Mutation in channelrhodopsin changing conformations causing damage to depolarization mechanisms
,o No action potentials created
Mutation in retinal pigment, causing no photoisomerization to occur
Homology between human eye and Chlamydomonas eyespot.
Could be homologous, currently unknown
Similar function, eyespot more simpler, eye more complex
Neither are more primitive
Definition of light
Most common definition: the portion of the electromagnetic spectrum that humans can detect with
their eyes
Relationship between wavelength and energy content of a photon.
Wavelength is inversely proportional to the energy content of a photon
Molecular characteristic of pigments that make them able to absorb light
Conjugated ring system, alternating single and double bonds
o Double bonds have nonbonding pi orbitals which allow for easy delocalization of electrons
Understanding of why biological systems only absorb visible wavelengths of the electromagnetic
spectrum
Visible light has the perfect amount of enery and wavelength to reach the earth's service.
Relationship between pigments and associated protein
Pigments are bound to proteins
oNot all proteins have pigments
Pigment absorption of light can result in conformational change to protein
Four “fates” of the excited state of chlorophyll resulting from absorption of photons.
1)Can lose it as heat, taking electron to ground state
2)Can lose a little as heat, dropping it to a lower low excited state, spitting out a photon through
fluorescence (allows it to glow red)
Fluorescence is a longer wavelength (less energy) than light used to excite molecule
3)Photochemistry: using energy from excitation to change the molecule/grow (eg. oxidation)
4)Can transfer the energy to excite a neighbouring pigment Luciferin + O2 + ATP Activated Luciferin
Luciferase
oNo transferring of electrons, just transferring excitation energy
Relationship between energy of photon and electron excited states to explain pigment colour and
absorption spectrum.
Electron’s excited state must match exactly that of the photon’s energy
Not absorbed wavelengths are what we see (reflected wavelengths)
Absorption spectra shows which wavelengths are absorbed
, Distinctions of photochemistry between phototransduction (vision, eyespot...) & photosynthesis
Phototransduction:
o Absorption of light into electrochemical signals
o Light absorption in pigment causes protein to have conformational change, allowing ion flow
through membrane
Photosynthesis:
o Converting light energy into chemical energy
o Uses energy transfer, but through the electron actually being transferred through the chain
o Eventually to oxidize chlorophyll
Major similarities and differences between phototransduction in eyespot vs eye
Eye:
o Retinal goes from cis to trans from light
o Indirectly opens and closes pores to the membrane
o Physical separation between where light absorbed and where ions flow
o Photoisomerization, therefore photochemistry
Eyespot:
o Retinal goes from trans to cis from light
o Directly opens pores to membrane
o Photoisomerization, therefore photochemistry
Role of endoplasmic reticulum bound ribosomes and free ribosomes
ER bound ribosomes produce secreted or membrane proteins
Free floating ribosomes make Points of control for regulation of protein abundance.
Factors affecting mRNA transcript abundance.
Rate of transcription
Rate of mRNA decay (protein breaking down)
o Balance of both
Characteristics of constitutive vs. induced vs. repressed gene (or protein) expression kinetics.
Constitutive Expression –stays the same (eg. Actin –housekeeping genes, required for cell to function
all the time)
Induced Expression –induced change in transcript/protein abundance (eg. HSP)
Repressed Expression–expression/abundance decreases (eg. some proteins that are repressed in
cancer cells)
Basic structure of an amino acid and what are the different classes of amino acids.
Central carbon, bonded to amino (NH3), carboxyl (COOH), a hydrogen (H) group, and an R group
(referred to as residues)
Nonpolar amino acids (A,V,L,I,G,C,F,W,M,P)
Characteristics of Chlamydomonas that make it a useful model system
Attributes of both plant and animal cells
Good for looking at light energy and information
Model system for photosynthesis, genetics, cell bio
Reproduces sexually and asexually
Easy to create mutants and effects of mutants are clearly seen
Haploid and relatively simple genome
Prokaryote and eukaryote genes in same cell (Nucleus and chloroplasts)
Relatedness of Chlamydomonas to plants and animals
Classified as protist, in chain leading to plants but is not a plant
Eukaryote, shares similarities to plants and animals
Phototransduction from Eyespot to Flagella
Photon hits eyespot, channel rhodopsin changes conformation, membrane becomes depolarized,
creating action potential, action potential travels down to flagella, channel rhodopsin closes and cell
membrane is repolarized, flagella takes action potential and performs photaxis
Advantages to Chlamydomonas in being phototactic
Decreases the chance of producing excess energy by moving away from light
Increases energy production efficiency by moving towards light when needed
Distinctions between primitive, complex, simple.
Primitive: genetically old
Complex: Many different and connected parts
Simple: Basic or uncomplicated
oEyespot is not more primitive than eye but is more simpler
Reasons why Chlamydomonas might move towards a light source.
Increase rate of photosynthesis
Reasons why Chlamydomonas might move away from a light source.
Too much light absorption could result in formation of ROS, resulting in harmful mutations
Has enough energy already, doesn’t need to spend more time doing photosynthesis
Light controls sexual activity; chalmy is sexually active
Possible mutations that could cause a Chlamydomonas cell not to be phototactic.
Mutation in channelrhodopsin changing conformations causing damage to depolarization mechanisms
,o No action potentials created
Mutation in retinal pigment, causing no photoisomerization to occur
Homology between human eye and Chlamydomonas eyespot.
Could be homologous, currently unknown
Similar function, eyespot more simpler, eye more complex
Neither are more primitive
Definition of light
Most common definition: the portion of the electromagnetic spectrum that humans can detect with
their eyes
Relationship between wavelength and energy content of a photon.
Wavelength is inversely proportional to the energy content of a photon
Molecular characteristic of pigments that make them able to absorb light
Conjugated ring system, alternating single and double bonds
o Double bonds have nonbonding pi orbitals which allow for easy delocalization of electrons
Understanding of why biological systems only absorb visible wavelengths of the electromagnetic
spectrum
Visible light has the perfect amount of enery and wavelength to reach the earth's service.
Relationship between pigments and associated protein
Pigments are bound to proteins
oNot all proteins have pigments
Pigment absorption of light can result in conformational change to protein
Four “fates” of the excited state of chlorophyll resulting from absorption of photons.
1)Can lose it as heat, taking electron to ground state
2)Can lose a little as heat, dropping it to a lower low excited state, spitting out a photon through
fluorescence (allows it to glow red)
Fluorescence is a longer wavelength (less energy) than light used to excite molecule
3)Photochemistry: using energy from excitation to change the molecule/grow (eg. oxidation)
4)Can transfer the energy to excite a neighbouring pigment Luciferin + O2 + ATP Activated Luciferin
Luciferase
oNo transferring of electrons, just transferring excitation energy
Relationship between energy of photon and electron excited states to explain pigment colour and
absorption spectrum.
Electron’s excited state must match exactly that of the photon’s energy
Not absorbed wavelengths are what we see (reflected wavelengths)
Absorption spectra shows which wavelengths are absorbed
, Distinctions of photochemistry between phototransduction (vision, eyespot...) & photosynthesis
Phototransduction:
o Absorption of light into electrochemical signals
o Light absorption in pigment causes protein to have conformational change, allowing ion flow
through membrane
Photosynthesis:
o Converting light energy into chemical energy
o Uses energy transfer, but through the electron actually being transferred through the chain
o Eventually to oxidize chlorophyll
Major similarities and differences between phototransduction in eyespot vs eye
Eye:
o Retinal goes from cis to trans from light
o Indirectly opens and closes pores to the membrane
o Physical separation between where light absorbed and where ions flow
o Photoisomerization, therefore photochemistry
Eyespot:
o Retinal goes from trans to cis from light
o Directly opens pores to membrane
o Photoisomerization, therefore photochemistry
Role of endoplasmic reticulum bound ribosomes and free ribosomes
ER bound ribosomes produce secreted or membrane proteins
Free floating ribosomes make Points of control for regulation of protein abundance.
Factors affecting mRNA transcript abundance.
Rate of transcription
Rate of mRNA decay (protein breaking down)
o Balance of both
Characteristics of constitutive vs. induced vs. repressed gene (or protein) expression kinetics.
Constitutive Expression –stays the same (eg. Actin –housekeeping genes, required for cell to function
all the time)
Induced Expression –induced change in transcript/protein abundance (eg. HSP)
Repressed Expression–expression/abundance decreases (eg. some proteins that are repressed in
cancer cells)
Basic structure of an amino acid and what are the different classes of amino acids.
Central carbon, bonded to amino (NH3), carboxyl (COOH), a hydrogen (H) group, and an R group
(referred to as residues)
Nonpolar amino acids (A,V,L,I,G,C,F,W,M,P)
