Midterm Flashcards
Provide the 4-point definition for autotrophy
- using light as a source of energy
- electrochemical gradient
- synthesis of ATP and NADPH
- synthesis of complex org mlcs from C
Why do all autotrophic organisms require a membrane-bound compartment?
To create a gradient that allows H+ to move through ATP synthase
What are the 8 components that all autotrophic organisms require to undergo autotrophic metabolism?
- membrane compartment
- an e- donating compound
- an e- transport chain
- mobile e- carriers
- proton pump
- ATP synthase complex
- mechanism to synthesize NADPH
- inorganic C fixation pathway (calvin cycle)
Distinguish the marine and terrestrial ecosystems on earth in terms of contribution to global C fixation
marine- 50%
terrestrial - 50%
Distinguish the marine and terrestrial ecosystems on earth in terms of source of biomass
marine- prokaryotes and algae >90%
terrestrial- plants ~80%
Distinguish the marine and terrestrial ecosystems on earth in terms of rate of biomass turnover
marine- 1 month
terrestrial- 12.2 yrs
Distinguish the marine and terrestrial ecosystems on earth in terms of nature of biomass turnover in terms of types of organisms and quantity of biomass.
marine- mostly chemoautotrophic and heterotrophic prokaryotes
terrestrial - mostly plants
What is the ecological ‘footprint’ of global agriculture?
ag uses 38% of earth’s land surface and 70% of fresh water
Provide a definition for a ‘source’ and ‘sink’ in plants. (b) Explain using examples how plants can be heterotrophic.
Source- net synthesis and export of sugars and other compounds (leaves)
Sink- net uptake and utilization of sugars and other organic compounds
What are the major organs found in plants?
-roots
-stems
-leaves
-floral
What are the major tissues found in plants
-epidermal
-ground
-vascular
What are meristems and their function in plants?
made up of unspecialized cells that can divide and become any type of cell in the plant.
-used for organ development and growth
What are the implications of a simple body plan in terms of plant function
greater developmental plasticity and totipotency
What are the implications of a non-motile whole-plant body in terms of plant function
has to invest resources into ways to deal with its environment as it cant move to a different location
What are the limits to resolution (i.e., how small we can see) for the following types of microscopy: (a) human eye; (b) conventional light microscopy; (c) high resolution (HR) confocal microscopy; (d) electron microscopy; (e) scanning probe techniques?
a. 100micrometres
b. <1 micrometer
c. <10nm
d.<0.1nm
e. 0.1nm
parasitic plant
plant that derives some or all of its nutritional requirements from another plant
haustorium
organ on a parasitic plant that connects them to the vascular system or hyphae of their host to extract nutrients
hemiparasitic versus holoparasitic
hemiparasitic- photosynthetic but also parasitic
holoparasitic- parasitic plant that is not capable of photosynthesis
epiparasitic
plants that feed on another parasite that is connect to a plant
obligate versus facultative parasites
obligate- need a host to complete their life cycle
facultative- can complete life cycle without a host
How is the definition for a ‘land plant’ affected by the existence of parasitic plants?
plants don’t need to have stems, leaves or roots
What is Striga sp. and its significance in agriculture?
parasitic plant that needs host for germination
-causes drought symptoms on the host plant
What are major events found in the Striga life cycle and factors that effect its establishment?
- host roots produce strigolactones
- striga detects these and hormones and parasitizes the plant underground
- striga produces an above ground shoot
- striga flowers and produces 0.5 mil seeds
- seeds go back into the soil and wait to be germinated
Describe how leaf cell anatomy is adapted for light interception and distribution in a leaf.
- epidermal cells act like a convex lens and focus light
- palisade cells channel light
- spongy mesophyll cells have air spaces- do light scattering and gas exchange
What are the major differences between plant cells and animal cells, and how do these differences in plant cells adapt them for autotrophy?
plants cells have…
1. a cellulose + hemicellulose cell wall
2. large vacuoles
3. cytosol confined to a thin layer between the tonoplast and cell wall
4. plastids, allow greater biosynthetic capability
In what ways are plant cells and animal cells similar?
both have a mitochondria, nucleus, golgi, ER, cell membrane
How are chloroplasts typically arranged in a mesophyll cell, and what is the functional significance of this arrangement?
arranged around air spaces
- this facilitates exchange of CO2 (gases diffuse 1000x slower in the cytosol versus air)
Why is a chloroplast considered a semi-autonomous organelle, and how does this adapt the plant for autotrophy?
They have their own DNA, and can self divide
How is chloroplast arrangement and structure adapted to its function in light interception?
-stores starch to use at night
-highly concentrated in the cell
-have a high membrane surface to volume ratio, enhancing light capture and metabolite transport
proplastid
undifferentiated plastid in meristematic cells
etioplast and function
partially differentiated plastid containing a prolamellar body
Function: turns into a chloroplast with light exposure
chloroplast and function
plastid that has the capacity for the light reactions
chromoplast
plastid that synthesizes and stores carotenoid pigments
-gives color to plants
leucoplast, including amyloplast, elaioplast and proteinoplast;
non pigment-containing plastid that synthesize and store compounds
amyloplast (starch)
elaioplast (oil)
proteinoplast (protein)
tannosome-forming chloroplast
produces tannins in a tannosome and releases them for storage in the vacuole
gerontoplast and dessicoplast.
plastids in senescing or desiccated tissues, respectively
Describe the steps involved in the synthesis and deposition of tannosomes.
- thylakoid membrane forms inflated thylakoids
- tannosomes pearl of the thylakoids
- multiple tannosomes are put in a shuttle that buds off the chloroplast
- shuttle carries them to the vacuole where they are incorporated by invagination of the tonoplast
- shuttle aggregate into tannin accretions stored in the vacuole
What is the function of the tannin synthesis and deposition system and why is this elaborate system required in the plant cell?
synthesizes tannin polymers without exposing them to the stroma and cytosol
What is a stromule and its potential function in the chloroplast?
stroma-filled tubules extending from a plastid
-import metabolites required for synthesis or export synthesized compounds
What are the 4 steps in the signal transduction pathway that regulates the positioning of chloroplasts in response to low or high light levels?
- phototropin is phosphorylated
- Ca2+ released into cytosol
- cp-actin redistributes to a leading edge
- chloroplast moves along actin filament
-chloroplasts associate with the PM through the KAC protein, cp-actin filaments, and the CHUP1 protein
What are the three membrane systems found in chloroplasts and one function for each membrane system.
- outer membrane
- inner membrane- separates stroma from the intermembrane space
- thylakoid membrane- Forms a network of thylakoids, arranged grana that contain chlorophyll and complexes
Why are thylakoid vesicles essential for photosynthesis?
They contain the chlorophyll
What are the 4 major membrane-bound thylakoid complexes found in the chloroplast?
- PSII
- cytochrome b6f
- PSI
- ATP synthase
Where is Rubisco found in the chloroplast?
in the stroma near CO2
Why are the 4 major complexes and Rubisco considered genetic chimeras?
they each have cells from plastid-encoded and nuclear-encoded DNA
Explain autotrophy in terms of the use of oxidized, inorganic precursors to synthesize reduced intermediary compounds, building blocks, macromolecules, assemblies, and organelles in plants
CO2, H20, NO3-/SO4^2- are used to synthesize ATP when is then used to build all the rest of the stuff? (pic at end of lec 1)
Define and differentiate between 1o and 2o plant metabolism in plants.
1o- essential metabolic processes for completion of the plant life cycle
2o- metabolic processes that facilitate but are not necessarily essential for completion of the plant life cycle
What role does respiration play in anabolic reactions in plants (discussed in class)?
it takes in oxygen and releases CO2 which is then used by the anabolic rxns in plants
Differentiate between plant metabolic and plant developmental processes in terms of the time frame required for their regulation
metabolic- seconds to days to adjust processes
developmental- hours to years to adjust processes
Differentiate between plant metabolic and plant developmental processes in terms of their importance for plant function.
both interact and area required for plant function but metabolic mechanisms are the “work horse” in living organisms
chemoautotrophic prokaryotes.
use chemical reactions to create organic compounds from carbon dioxide.
-electron flow is establish through oxidation of reduced inorganic compounds
Provide 5 groupings of chemoautotrophic bacteria, and their source of energy and ecological significance.
- nitrifying bacteria: ammonium and nitrite, nitrification in the global biogeochemical N cycle
- anammox bacteria: ammonium, produce 50% of global N2
- nonphotosynthetic sulfur bacteria: H2S, global S cycle
- Iron bacteria: Fe2+, global Fe cycle
- hydrogen bacteria: H2, microaerophilic, anaerobic and hyperthermophilic environments
In what extreme environments can chemoautotrophs be found?
places with high temp, acidity and pressure
ex. deep sea
What are nitrifying bacteria, including the reaction they catalyze, cellular characteristics, and ecological role?
use inorganic chemicals as an energy source
turn ammonia to nitrite (nitrosifyers) then nitrite to nitrate (nitrifiers)
Syntrophy? including its significance to the nitrification process?
the pairing of multiple bacterial species to achieve a chem rxn that on its own is energetically unfavorable
-allow ammonia to be turned into nitrate
Explain how genome sequencing contributed to our understanding of metabolism in Nitrosomonas europaea, including the limitations of this experimental approach.
allowed us to see a diagram of how the different systems work together?
Why does Nitrosomonas europaea require an extensive transporter system for iron?
iron is important for the system?
-extensive transport systems make up 11.5% of the genome
Why is the citric acid cycle considered anabolic in autotrophic organisms?
the cycle is anabolic in nature
-The cycle can be reversed to utilize key intermediates for the biosynthesis of various cellular components like amino acids and fatty acids, effectively building up organic molecules from carbon dioxide through the process of carbon fixation.
Explain the functional significance of forward and reverse electron transport in Nitrosomonas europaea.
forward transport- required for the ETC and ATP synthesis
reverse transport - required for NADH production?
What are the 8 specific components found in Nitrosomonas europaea that allow autotrophic metabolism?
- membrane compartment
- e- donating compound
- ETC
- mobile e- carriers
- proton pumps
- NAD(P)H synthesis
- ATP synthesis
- reductive inorganic C fixation pathway
What are 2 factors that limited the spread of chemoautotrophic organisms on earth?
- use inorganic sources for energy but they only have a small amount of free energy in comparison to glucose and hexadecane
- the inorganic compounds are found in specific environments
photoautotrophy
the ability to intercept and utilize light energy to initiate a flow of e-
-another name for phosyn
What is the ecological/evolutionary significance of photoautotrophy?
allowed for the development of complex life forms and an oxygenated atmosphere
source of energy and the source of electrons for anoxygenic photoorganoautotrophs
uses acetate, succinate or lactate as the e- donor
source of energy and the source of electrons for oxygenic photoautotrophs
sunlight is the source energy and uses H2O as the e- donor
source of energy and the source of electrons for anoxygenic photolithoautotroph
sunlight is the source of energy and uses H2S, Fe2+, or H2 as the e- donor
Why do organisms that use anoxygenic photoautotrophy only require one photosystem
H2S requires less energy to split than H2O
What are the two major genera of cyanobacteria found in the ocean and their overall contribution to marine photosynthesis?
Prochlorococcus - 5% of global phosyn
and Synechococcus
What are 4 characteristics shared by cyanobacteria?
contain chlorophyll a, beta-carotene, carboxysomes, and store glycogen
What major difference exists between most cyanobacteria (including Synechococcus) and the prochlorophytes?
Most genus have phycobilisomes which is a specialized light-harvesting complex
prochlorophytes have chl b
What is the ecological significance of Prochlorococcus?
they are the smallest and most abundant photoautotroph on earth
What is the ecological/evolutionary significance of oxygenic photoautotrophy apart from oxygen evolution?
the development of oxygenic photoautotrophy led to rapid growth because light and water is everywhere
What are the different taxonomic groups of oxygenic photoautotrophs and how can they be distinguished based on pigment composition?
viridiplantae (plants and green algae) - have chlorophyll- a,b and carotenoids
chromista - have chlorophyll- a,c and carotenoids
biliphyta (red algae) - have chlorophyll a, carotenoids, and phycobilins
eubacteria (cyanobacteria) - have chlorophyll- a, b, d, f, carotenoids and phycobilins
Describe endosymbiosis of plastids in eukaryotes
a free-living photoautotrophic organism is phagocytized and converted to a stable endosymbiont
Describe primary endosymbiosis of plastids in eukaryotes
involves a prokaryotic symbiont
complex situation involving many nuclear gene donors
-these plastids have 2 membranes
Describe complex endosymbiosis of plastids in eukaryotes
involves a red or green algal symbiont
-complex
-these plastids have 3-5 membranes
List three ‘odd ball’ organisms that provide evidence for 1o endosymbiosis of plastids, including the nature of the evidence.
Paulinella- contains a peptidogylcan layer and carboxysomes like cyanobacteria
Glaucophytic algae- has a peptidoglycan layer in plastid and phycobilisomes like cyanobacteria
Rhopalodiaceae- its spheroid body shares traits with cyanobacteria
List three ‘odd ball’ organisms that provide evidence for complex endosymbiosis of plastids, including the nature of the evidence.
chloroarachniphytes- have a plastid with 4 membranes, nucleomorph contains green algal nuclear genes
cryptomonads have a plastid with 4 membranes. nucleomorph contains red algal nuclear genes
dinoflagellate- has both a host nucleus and nucleus from the diatom symbiont and 5 membranes
Discuss the ecological significance of organisms in Kingdom Chromista (i.e., chromists).
Diatoms- have silica cell wall in 2 halves, CO2 conc. mech. in pyrenoids ~40-45% of marine PN ~100,000 species
Coccolithophorids- ~25% of C transport to deep sea
Dinoflagellates- many are photosynthetic symbionts in coral reefs, cause red tides, some bioluminescent
Provide 4 reasons why the silica cell wall has contributed to the success of diatoms.
- relative abundance of Si
- strong and protective
- less energy to synthesize verses organic cell walls
- silica depositing machinery is very flexible morphologically
What are 4 other reasons why diatoms have been so successful? ( not including silica cell walls)
- metabolic flexibility- adapt to low/high light
- large central vacuoles for nutrient storage, biochemical defences, and CO2 conc. mech.
- ability to change their depth in water through cell conglomeration and production of heavy spores under unfavourable conditions
What characteristics are shared by organisms in Kingdom Plantae?
-plastid derived from a primary symbiont
-plastid has 2 membranes and contacts cytosol, chl a and carotenoids
What characteristics are shared by all terrestrial plants?
ability to live on land and retention of embryo
-waterproof cuticle
-alternation of generations
Compare and contrast the Subkingdoms Biliphyta and Viridiplantae.
Biliphyta- chloroplast has phycobilisomes, lutein, thylakoids unstacked; store cytosolic starch, plastid codes for ~140-200 proteins, aquatic
Viridiplantae- chl b, zeaxanthin and lutein, stacked thylakoids, store starch in plastids, plastid codes for ~100 proteins
Compare and contrast the red algae, glaucophytes and ‘green plants’.
red algae- no flagella or centrioles; store Floridean starch, plastid codes for ~200 proteins
glaucophytes- store plant-like starch, plastid codes for ~140 proteins
green plants- cell wall with cellulose and hemicellulose, waterproof cuticle, apical meristem, retention of embryo, alternation of generations, granal and intergranal thylakoids in phosyn species
When is plastid replication required in plant cells?
- cell division- to ensure segregation
- cell expansion and differentiation- to generate large numbers of plastids
Describe the process of plastid replication in eukaryotic plastids, including any similarities and differences from bacteria.
unicellular algae contain one or a small # of plastids that divide once per cycle
- both use ARC6 and ARC5 proteins
Describe how plastid replication is regulated in green algae and higher plants.
in land plants, all genes involved in plastid division are nucleus encoded.
regulated by ARC6 that affects proplastid # and size in meristems and mesophyll cells and ARC5 that effects plastid division in mesophyll cells but not proplastids
Provide a comprehensive definition for a plastid.
a plastid is an organelle that originated directly or indirectly from a primary endosymbiosis that:
1. is found in all photoautotrophic and in some heterotrophic eukaryotes
2. is semi-autonomous
3. contains at least 2 membrane systems that interact with the ER
4. role in the synthesis and storage of biomolecules
In what ways is the photosynthetic apparatus in a plant analogous to a solar hydrogen fuel cell?
both have
1. and interception of solar energy
2. coupling of solar energy to splitting of water, releasing H+, e- and O2
3. utilization of energy in H and e- for work
4. energy storage for dark periods
Why do we need to study the photosynthetic apparatus at the molecular level to fully establish its structure and function?
because nature constructed the phosyn apparatus at the nanoscale level
What are the 3 functions for chlorophyll/bacteriochlorophyll in photoautotrophs? Distinguish between energy transfer and electron transfer in your answer
- absorbs light energy in the LCH
- transfers exciton energy with high quantum efficiency to the RC (energy transfer)
- does primary charge separation across the phosyn membrane (e- transfer) which initiates e- transport that leads to an electrochemical gradient and ATP and NADPH synthesis
How are bacteriochlorophylls similar and different from chlorophylls?
-both have a tetrapyrrole ring with Mg2+ in the center with 4N around
-bacteriochlorophylls split H2S instead of H2O
-bcs absorb in the infrared range instead of the visible range
How is the structure of chlorophyll related to its function?
the resonating structure (4 pyrroles) provides stability, but it makes the tetrapyrrole ring reactive
In what components is chlorophyll found in oxygenic and anoxygenic photoautotrophs?
in oxygenic photoautotrophs chl a and b are found
What is the significance of the resonant structure in chlorophyll, including the number of double bonds in the chlorophyll molecule?
the resonating structure (4 pyrroles) provides stability, but it makes the tetrapyrrole ring reactiv
What are functions for Mg in chlorophyll?
- balances the 2- charge of the tetrapyrrole ring
- keeps the tetrapyrrole ring rigid so the absorbed photon energy is not easily dissipated by thermal vibrations
- helps position chl mlcs within the LHC proteins through non-covalent bonds including H-bonding
What are the major species of chlorophyll found in oxygenic photoautotrophs?
chl a and chl b
What species of chlorophyll are found in land plants, Chromista, and cyanobacteria?
cyanobacteria- chl a,b,d,f
What is the significance of the discovery of chl d and chl f in cyanobacterium?
its found in cyanobacteria in environments with a lot of far-red light, they increase the PAR up to 19% in these cyanobacteria
What are the major species of bacteriochlorophyll, and in what organisms are they found?
Bchl a,b,c,d,e -they are found in anoxygenic photoautotrophs
How are bacteriochlorophylls similar and different from chlorophylls?
BChl are like phytochlorins
What is a carotenoid and distinguish between xanthophylls and carotenes
they are accessory pigments that are important for light absorption and regulating ROS
oxygenated carotenoids = xanthophylls
non-oxygenated = carotenes (beta-carotene)
In which organisms are carotenoids very important as an accessory pigment for light absorption
dinoflagellates, heterokonts and anoxygenic photoautotrophs
Explain how the structure of a carotenoid relates to its functions?
carotenoids have many double bonds which help with absorption in visible range, long 40 C structure, and hydrophobic allowing insertion in membranes
Why do all oxygenic photoautotrophs have carotenoids?
because they need them for light absorption and to regulate ROS
What are the functions for carotenoids in the photosystem of terrestrial plants?
for light absorption and to regulate ROS
Describe the absorbance spectrum for an intact leaf in a land plant.
strong in the red and blue wavelengths and less in the green and yellow
How does the absorbance spectrum for a leaf compare to the terrestrial light spectrum?
the light-harvesting apparatus in land plants is adapted to the wavelengths in the terrestrial environment
-will absorb far-red and infra-red in envirn. where it is enriched like shade
What is the functional significance of reduced absorption of green light by the photosynthetic apparatus in terrestrial plants?
at higher light intensities, green light has the highest efficiency of CO2 fixed per available photon
What is a chromophore?
molecules that absorb light at specific wavelengths and give color to objects.
ex- chls and carotenoids
What is the specific definition for a ‘pigment’ as found in photoautotrophs?
chromophore + protein
How does light absorption differ between chlorophyll chromophores and the chlorophyll-protein complex in plant photosystems?
chlorophyll chromophores are governed in part by proteins to which they are non-covalently bound
What are the basic characteristics of the LHC-IIb monomer?
- 3 membrane-spanning hydrophobic helices
- 2 lutein that stabilize the LHC
- chl a’s close to chl b’s in 2 layers that non-covalently associate with a.a. … fast energy transfer
- xanthophylls neoxanthin and violaxanthin
How is the structure of the LHC-IIb monomer related to its function?
its structure lets it have fast energy transfer and lets it dissipate ROS
What are characteristics of LHCIIb trimers found in chloroplasts?
8 LHC trimers surround each PSII complex like an antenna network to increase the light absorption surface of PSII
Explain how Photosystem II is designed in plants, including the arrangement of LHC complexes relative to the core antenna and reaction center.
8 LHC trimers surround each PSII complex like an antenna network to increase the light absorption surface of PSII
What is the order of energy transfer between LHC pigments to the reaction centers in plants?
carotenoids to chl b to chl a to PSII (P680)
How does the order of energy transfer between pigments explained relate to their absorption characteristics?
carotenoids have the most photon absorption (energy) then energy gets lost as heat as it goes down the chain
What is the functional significance of this specific order of energy transfer?
The light hits the carotenoids then it moves down to chl a and chl b then goes to the RC at the end of the energy gradient
What is the extinction coefficient for chlorophyll and explain how this parameter shows that chlorophyll is well designed for its function?
~100,000 L/mol/cm for chlorophyll at 625cm this allows for efficient light absorption
Why can chlorophyll exist at higher concentration in a thylakoid membrane compared to an organic solvent (discussed in class)?
because they are in a staked thylakoid so can be in contact with more light?
What are 4 properties of chlorophyll/bacteriochlorophyll that make them efficient light absorbers?
- the absorption spectra match with the long wavelengths of light found in sunlight owing to the large # of resonating double bonds in the tetrapyrrole ring
- they can associate non-covalently at high conc. with other chlorophyll mlcs, the thylakod membrane, and with LHC proteins to allow fast energy transfer
- the extinction coefficients are very high= efficient light absorption
- they have a relatively slow rate of fluorescence, which is essential for energy transfer to the RC
What is a photosystem and its function in photoautotrophs?
an association of
-LHCs
-a core antenna
-a reaction center
purpose is to create a photochemical event to initiate e- transport and use the energy to synthesize ATP and NADPH
What are the three components found in a photosystem?
-LHCs
-a core antenna
-a reaction center
What are the 4 major sets of components found in PSII and their function?
- several preipheral LCHII complexes
- core antenna consisting of Chl binding proteins
- D1/D2 reaction center complex- where e- transport initiates and several e- transporters reside
- water splitting complex (MSP or oxygen evolving complex (OEC))
How does the arrangement of the 4 major sets of components in PSII relate to their function?
The core antenna and reaction center exists as a dimer (two copies of each in PSII), and surrounding these dimers are 8 LHCII complexes. 4 LHCII complexes associate closely with the core antenna+reaction center, and the other 4 are loosely associated.
What data show that 4 LHCII-b trimers are tightly associated with PSII, and 4 LHCII-b trimers are lightly bound?
microscopy using x-ray diffraction let scientists see a top view of PSII and see where the trimers are located
What is the functional significance of this association between the LHCII-b trimers and the photosystems?
that LHCII can move between PSI and PSII, and the loose binding of 4 LHCII facilitate this movement of LHCII between photosystems.
What is the Emerson enhancement effect and what did these experiments demonstrate about the photosynthetic apparatus in oxygenic photoautotrophs?
The experiments provided evidence that more than one photosystem was present, since either red or far-red light induced O2 evolution, but when provided together the effect was synergistic and not simply additive.
What is a phycobilisome and distinguish Synechococcus and Prochlorococcus according to whether they have a phycobilisome?
phycobilisomes are a peripheral antenna system that operate in an oxygenic environment
Synechococcus contains phycobilisomes
Prochlorococcus
Prochlorococcus contain a different set of chromophores that reflect the light quality in their environment.
Compare and contrast the photosystem in Synechococcus and Prochlorococcus, and how each is adapted to its environment?
PSII in Synechococcus has phycobilisomes that are attached to the core antenna that absorbs blue and green light
PSII in Prochlorococcus dont have phycobilisomes and have divinyl chl a, b that absorb blue
What is a phycobilin chromophore and its properties.
they are accessory pigments tat extend the absorption spectra not absorbed effectively by chl
phycobilin chromophores bind covalently to phycobilin proteins to form an open tetrapyrrole ring
In which photoautotrophic organisms are they found?
aquatic photoautotrophs
- some cyanobacteria in phycobilisomes
-red algae and glaucophytes in phycobilisomes
-cryptophytes (in thylakoid lumen without phycobilisomes)
What are the three phycobilin pigments?
- PE
- PC
- AP
What similarities and differences exist between phycobilin and chlorophyll pigments?
Why are phycobilin pigments found in certain cyanobacteria and red algae?
Phycobilins are nature’s solution to making a tetrapyrrole ring that is water-soluble.
Explain how the phycobilisome ‘antenna network’ is designed, including the arrangement of the phycobilin pigments.
arranged going from PE to PC to AP, with allophycocyanin forming the core antenna in the structure
What is the functional significance of the arrangement of phycobilin pigments in a phycobilisome?
The peak wavelengths absorbed for each phycobilin are ordered from the short wavelength (on the exterior) to the longest wavelength absorbed (on the interior). This arrangement provides multiple pigments and allows energy to move down the energy gradient from higher to lower energy, which supports a fast rate of energy transfer to the reaction center.
How does water attenuate solar radiation?
different wavelengths of light are differentially absorbed as they pass through a water column.
wavelengths with higher and lower energy (relative to green & blue light) get attenuated in the water column, and thus the relative proportion of different wavelengths of light changes as depth of water changes.
Provide examples of how the absorption spectra of photoautotrophic organisms correspond to the available light spectra.
In prochlorococcus and Synechococcus their absorption spectra in its LHC matches up with the prevailing light in the environment
Describe the light-harvesting apparatus in purple bacteria based on the chromophores and pigments present
It has two chromophore-protein complexes -LH1 and LH2
Describe the light-harvesting apparatus in purple bacteria based on the arrangement of LH complexes relative to the core antenna and reaction center
The LH complexes are arranged in a circular pattern, which supports fast energy transfer to the reaction center.
Describe the light-harvesting apparatus in purple bacteria based on the influence of light intensity on arrangement of the LH complexes.
Light intensity effects the proportion of LH2 to LH1
In low light the proportion of LH1 decreases, which reflects the important role of LH2 in light interception in purple bacteria.
How does the photosystem in purple bacteria adapt them to their environment?
It allows two absorption bands (800 and 850nm) with only one chromophore
-this allows them to live in environments enriched in far-red and green light
How is the light-harvesting apparatus in chlorosome-containing bacteria designed?
chlorosomes are large and surround the entire perimeter of a cell
What groups of organisms contain chlorosomes, and what is the adaptive significance of chlorosomes in these organisms?
anoxygenic bacteria
-allows absorption of infra-red light at very low light intensities
luminescence
emission of light from a substance
chemiluminescence
a type of luminescence caused by a chemical reaction as opposed to light absorption
bioluminescence
a type of chemiluminescence that requires an enzymatic reaction like luciferase
photoluminescence
ability of a substance to absorb light and emit light of a longer wavelength/ lower energy
fluorescence
type of photoluminescence that occurs in 0.01-20 ns for organic mlcs
phosphorescence
type of photoluminescence that occurs in 10^-3 to 100s
What are the differences between fluorescence and phosphorescence?
Both the mechanism of photoluminescence and the rate constant differ for these phenomenon; they are both relevant to energy absorption and transfer in a photosystem
phosphorescence is dangerous bc absorbed energy lasts too long in a stable state so can make ROS
What equation describes the initial step in transduction of light energy to chemical energy?
pigment (e- at lowest energy ground state) to pigment (excited state- e- shifted to a higher energy orbital)
What is meant by the 1st and 2nd excited singlet state for chlorophyll?
1st state= red absorption band
2nd state= blue absorption band
each excited singlet state is equivalent in energy to the photon wavelength absorbed
If an electron moves to a slightly higher energy than the excited singlet state, it loses energy through vibrational relaxation to reach the excited singlet state
How is the 3rd excited triplet state for chlorophyll formed (3Chl), and what is its significance?
this excited state can result in phosphorescence when the electron moves to the ground state. Since phosphorescence takes much longer to occur compared to fluorescence, there is a greater probability that the energy can be transferred to an O2 molecular, resulting in a reactive oxygen species.
What are the 6 potential fates for excitation energy?
- 2nd excited state is unstable (<10^-12s)
- transfer of energy between chromophores to the reaction center is non-enzymatic (10^-13s)
- photochemistry (~3.5x10^-12s)
- fluorescence- 1st singlet state lasts ~7 x 10^-9s
- loss of energy as heat
- ROS, energy lost as phosphorescence
Considering the 6 options in (10) above for electrons falling to their ground state, why does most of the energy go towards the photochemical reaction (can be up to 95% of the photons captured by a photosystem). Your answer should demonstrate how ‘timing is key’ in energy transfer from the LHC to the reaction center of the photosystem.
because it takes the shortest amount of time ?
What is the general equation that describes a photochemical event?
pigment (ground state) +acceptor to pigment(excited state) +acceptor to pigment (oxidized state) +acceptor(reduced state)
What replenishes the electron lost from the reaction center after a photochemical event occurs?
another e- replaces it that comes from water
Define quantum yield and what are synonymous terms used to describe this parameter.
it is the efficiency of a PS
-# photochemical products/ # photons absorbed
Explain the technique developed by Deisenhofer, Michel, and Huber for determining the 3-dimensional structure of membrane-bound proteins.
the technique allowed isolation and crystallization of membrane-bound proteins using detergents with hydrophilic and hydrophobic ends. The detergent solubilized the membrane-bound complex and created micelles, which created a crystalline structure sufficient for x-ray crystallography.
-did this on the reaction center
What is the structure of the reaction center complex in purple bacteria according to the location in the photosystem and protein structure
It resembles PSII in land plants.
complex consisted of protein components that allowed the chromophores to position correctly by providing a scaffold for the aromatic groups and the associated Fe ion. The positioning of the reaction center complex is within the LH1 complex. reaction center complex is a heterodimer and consists of L/M subunits
What is the structure of the reaction center complex in purple bacteria according to the order and arrangement of electron carriers?
the reaction center exists as a heterodimer ( M and L subunits + e- carriers)
What are forward and reverse electron transport and how do they compare between the chemoautotroph Nitrosomonas (discussed in Lecture 2) and purple non-S bacteria?
green plants
forward- making of an electrochemical gradient for ATP synthesis
reverse- uses part of the electrochemical gradient to generate NADH by reversing the direction that H+ are normally pumped
chemoautotroph
forward transport- required for the ETC and ATP synthesis
reverse transport - required for NADH production?
What is the sequence of electron movement within PSII of plants beginning with H2O and ending with QB?
movements in P680 occur fastest and 1st
the OEC to PD1 is intermediate
QA to QB is slowest and last
How do the rate constants compare for the various steps in electron transport in PSII?
movements in P680 (10^-12 - 10^-9)
QA and QB (10^-6 - 10^-3)
Why do oxygenic photoautotrophs have a D1/D2-type PSII?
the type is required for splitting H2O by the OEC
What is the structure and function of the OEC in PSII, and how are the structure and function related?
structure = Mn4O5Ca
function = water-oxidizing catalyst that splits H2O
What methodology has been used to determine the various electron carriers in an electron transport chain?
Since the major complexes in the thylakoid membrane are nanometers apart, simple diffusion of an electron cannot occur at a sufficient rate
mobile electron carriers can diffuse at a sufficient rate between complexes.
What methodology has been used to determine the rates of the electron transfer reactions?
The charge separation at the reaction center must occur within ~10-9 s to ensure that a photochemical event occurs.
the distance cannot be more than 10 Angstroms for this to occur within that time frame
Provide a biophysical reason that explains why mobile electron carriers are required in the electron transport chain.
Since the major complexes in the thylakoid membrane are nanometers apart, simple diffusion of an electron cannot occur at a sufficient rate
mobile electron carriers can diffuse at a sufficient rate between complexes.
What is the function of the cytb6/f complex?
function is to move H+ between the stroma and lumen
What mobile electron carriers interact with the cytb6/f complex?
PQ gives e- to cytb6/f and then PC shuttles them away
What are the functions of PS I in plants?
to get energy from photons and donate it to e-s?
What is meant by the term P700 in photosystem I?
absorbs light in the 700nm wavelength
What is the basic chemical equation for the light reactions in photosynthesis?
8 photons + 2 H2O to 1 O2 + 2 NADPH2 + 3 ATP
typically 9.5 photons
Why are more than 8 photons typically required per 2 H2O split in the light reactions?
9.5 photons/ O2 are usually required because the quantum yield of PSII runs at 85% efficiency
How many photons are required per 3 ATP synthesized in the chloroplast if the quantum yield is 1.00?
8
How will the value change for the # photons required per 3 ATP synthesized if the quantum yield is less than one?
it will increase and is usually around 9.5
How many ATP are formed per one turn of the ATP synthase, and what is the significance of this stoichiometry to photosynthesis?
3 ATP
the ATP synthase uses 4 H+ for each ATP produced, and thus 3 ATP can be produced per O2 released (and 2 H2O split). The fixation of one CO2 requires 3 ATP in land plants, and thus the stoichiometry is correct.
What is the rate limiting step in the chloroplast electron transport chain in plants?
the step where reduced PQH2 donates its electrons to cytb6/f.
100-300 photochemical events per reaction center per second. This rate is much lower than the required rate of energy transfer to the reaction center
Explain why oxygenic photoautotrophs require two photosystems and anoxygenic photoautotrophs only require one photosystem based on standard reduction potential and energy requirement to split either H2O or H2S.
The standard reduction potential of H2O (used by oxygenic photoautotrophs) and H2S (used by anoxygenic photoautotrophs) is quite different. H2O is much more difficult to oxidize (split) based on its standard reduction potential, and ~3X more energy input is required. To satisfy this 3X greater energy requirement, two things occur: (1) 2X more photons are absorbed by having two photosystems; and (2) photons 1.5X higher in energy are absorbed
What is the Mitchell chemiosmotic model for ATP synthesis?
In chloroplasts, a H+ gradient across the thylakoid membrane is required for ATP synthesis.
What experiment did Jagendorf et al. perform that provided the 1st evidence for the Mitchell model?
This was first demonstrated by Jagendorf using isolated chloroplasts. The hypothesis tested the hypothesis that a pH gradient was required to synthesize ATP. By manipulating pH, Jagendorf’s lab was able to obtain data supporting the hypothesis.
What is the molecular structure of the ATP synthase found on the chloroplast inner membrane and how does it relate to its function?
ATP synthase has subunits that spin like an electric motor to pump H+
What are the major sources of reactive oxygen species (ROS) in plants?
- PSII and PSI
- chloroplastic and mitochondrial ETCs
- peroxisome produces H2O2
- apoplast during cell wall formation
- membranes like PM and ER
What damage is caused by ROS in the cell, and why is ROS regulation in a plant cell necessary?
ROS damages DNA, protein and lipids
-regulation in necessary because ROS act as a signal to initiate cellular responses to plant stress
Why are ROS central to stress physiology in plants?
ROS act as a signal to initiate cellular responses to plant stress
Explain why ROS are required for plant function.
are a regulatory signal at low levels for photosynthesis, stomatal movement, cell cycle, growth and development, and senescence
What is Q10 and its biochemical and physiological significance in plants?
Q10 is defined as the change in rate of a biological process with a 10 Celsius degrees change in temperature.
-a Q10 = 2 indicates that the rate of a biological process will change by a factor of 2 for a 10 Celsius degree change in temperature
Explain how an imbalance can occur between the # photons absorbed by a photosystem and the ability to use the energy for plant processes including photosynthesis.
An imbalance between electron transport and photosynthetic C metabolism can occur at low temperature since the Q10 for electron transport is close to 1, whereas the Q10 for photosynthetic C metabolism is ~2.
- under the temperature range that allows plant growth, the rate of e- transport through the chloroplastic e- transport chain is not affected by temperature and thus it continues at the same rate even at low temperatures for a given light level. In contrast, the rate of photosynthetic C metabolism is sensitive to temperature owing to the enzymes required, and their activity decreases as the temperature decreases.
What are the 3 major lines of defense used by plants to dissipate excess light
1st. quenching of excess excitation as heat
2nd. scavenging of toxic photoproducts
3rd. D1 excised, D1 degraded
What are the major reactive species formed in plants and how are they formed?
O2 - superoxide anion
H2O2 -hydrogen peroxide
OH -very reactive hydroxide radical
1O2 -singlet oxygen from 3Chl
formed by e- addition
What are the two basic categories of ROS scavenging systems in plants?
- enzyme systems and water soluble antioxidants (ascorbate, glutathione)
- membrane-bound carotenoids and tocopherol (hydrophobic antioxidants)
List the major enzymes and antioxidants utilized by plants to scavenge ROS.
- enzyme systems and water soluble antioxidants (ascorbate, glutathione)
- membrane-bound carotenoids and tocopherol (hydrophobic antioxidants)
Why do all oxygenic photoautotrophs have carotenoids?
to dissipate excess light energy and to reduce ROS
What are the functions for carotenoids in the photosystem of terrestrial plants
- for photoprotection via quenching of triplet Chl to reduce singlet oxygen
- singlet oxygen scavenging by neoxanthin
- non-photochemical quenching by the violaxanthin cycle to release excess energy as heat
What is the violaxanthin cycle in plants and its function?
forms zeaxanthin from violaxanthin which makes CP26 more susceptible to a decrease in pH
What is non-photochemical quenching (NPQ) and its role in the photosynthetic apparatus?
the release of excess excitation energy as heat
What are the three components of NPQ and their function in NPQ?
- energy-dependent quenching
- ZE-dependent quenching by the violaxanthin cycle
- photo inhibitory quenching due to inactivation/ degradation of DI protein
What two components of quenching that effect fluorescence but not NPQ?
- chloroplast movement
- state-transition quenching by separation of LHC from PSII
What is the significance of state-transition quenching (qT) phosphorylation/ dephosphorylation of LHCII for chloroplast function?
State-transition quenching (qT) is involved in reducing the amount of light absorbed by PSII. The basis for this mechanism is the movement of LHCII from PSII to PSI to change the proportion of available light absorbed by each photosystem.
What enzymes are required for the phosphorylation/ dephosphorylation of LHCII and how is the phosphorylation state of LHCII regulated?
Compare and contrast non-cyclic electron transport with cyclic electron transport in the chloroplast based on the following parameters:
non-cyclic: both ATP and NADPH produced in a 3:2 ratio
cyclic: Ferredoxin donates e- from PS I to a Fd-PQ oxido-reductase, forming PQH2, which donates e- to cytb6 allowing H+ pumping - ATP produced but no NADPH
