week 5 LHC II and PS II structure

what happens when the light energy is low in terms of the e- being transported and hence the other processes which rely on this ?

the e- trasnport is very slow , since there is not enough photon energy, hence light energy which can be used, which means that the reduction of NADP is not possible, and hence the production of ATP is not possible?

what does the antenna do when the light intensity is low ? how is this possible , what allows the antenna to sense that light is low ? and how can the antenna do this ?

the antenna increases its size, this happens because the genome senses that there is a change in the light intensity due to the slow down of the e- trasnport.

The antenna can change the size because of its modular organization , which allows it to vary in sizes from 8 to 8 trimeric units of LHCII per RC. = this in turn makes 80 to 350 Chl per one RC increasing significantly the amount of pigments= enahcning the probability of them absorbing light.

what is a long term adapatation of plants to low light ?

the plants build a larger antenna = this is slow because it takes days/ hours, since is an acclimation process.

why do we need to control the light reaction of photosynthesis ?

There are PSII and PSI, which absorb light energy at different wavelengths, which means that, since the light intensity which reaches them can vary, in the shape PS I absorbs more light and in the sun, PSII does; this difference in absorption creates a frequency imbalance in light energy input into the RC= which decreases the e- transfer efficiency = hence the quantum yield of photosynthesis decreases.

Therefore, these reactions need to be controlled so that the plant can have mechanisms by which it can defend itself from excess light or too low light, as well as prevent the imbalance in energy transfer.

what happens when the plant receives too much energy from light? Mention the process and describe how the RC resembles a mean mincer.

When the light intensity increases, as well as the energy, the antenna enters dissipative mode.

Once this happens, if the plant does not deal with it, then photoinhibition happens which shows that the RC cannot deal with the excess of energy input.

The excess energy will cause the pigments to get excited, and photoinhibition happens, where there will be spillage of excess e- = This affects the antenna negatively, causing a decrease in size, and this is not rapid or efficient at high light intensities to be used as a defending mechanism.

What are the regulatory mechanisms used by the plant to balance and stabilise the photosynthetic process? what is the reason why the regulatory mechanisms exits?

The two regulatory mechanisms used are state transition ( which is a short-term adaptation to low light), and NPQ ( which is a short-term mechanism for high light intensities)

The reason why the plant needs regulatory mechanisms is because it lives in a fluctuating environment and it has a fixed composition. Hence they need to use these mechanisms to extend the conditions over which they can remain balanced.

what are the two main enzymes which act in the state transition mechanism and what do they do and to what do they respond ?

to what does the p-LHCII bind when it moves away from the LHCII (PSII)

• Membrane-bound kinases = are activated when the pool of quinone is reduced, which happens when PSII gets more light than PSI, this is sensed, and hence, the PQH2 will bind to the kinase.

  This causes the kinase to phosphorylate trimers of significant pigments in the antenna. The trimers become negatively charged, which causes them to be repelled from the LHC II. Hence, they will attach themselves to the PSI, but this is only possible in the presence of PSI-H.

• Phosphorylase = these enzymes detect when the PQ + is oxidised, which happens when PSI gets more light than PSII, and the PQ+ binds the phosphorylase.

  The enzyme then dephosphorylated the p-LHCII =, causing the trimers to return to the LHCII, reduce the antenna size of PSI, and increase the antenna size of PSII, too.

• p-LHCII binds to the RC of the PSI = to 4 subunits.

explain the dual function of H+ when it comes to NPQ, and mention the way this mechanism works as well as what the recent discovery showed about what acts as an energy sink?

• When there is excess light intensity there will be an accumulation of H+ on the stromal side, which causes acidification, which can damage the plant.

• The excess of H+ will signal to the plant that there is too much energy and that NPQ needs to take place = hence why we can say that this process is a feedback mechanism)

• H+ has a dual role = they can interact directly on LHCII, causing the excess energy to be dissipated as heat, or they can cause the activation of deepoxidase enzyme, which removes the two epoxy oxygens in violaxanthin, converting it to zeaxanthin.

• This change from violaxanthin to zeaxanthin causes conformational changes to the protein, and hence, there are changes to the interactions between the pigments, which in turn will increase the interaction between Chl a and lutein 1

• This increased interaction, int he dissipative state of the LHCII, will allow the energy transferred from the Chla to lutein 1 to go into the forbidden S1 state of lutein 1, which is then dissipated by internal conversion as heat.

what is the function of RC ? what are the different types of RC and how are they different ?

Convert light energy into chemical energy.

There are 2 types of RC:

Type 1=, which is used as carriers of iron-sulfur centres and ferredoxin

Type 2 is used as an e-carrier, pheophytin and quinone.

They are similar in terms of their function and what they do.

are type I and type II highly conserved ? how do we know this ? why do green sulfur bacteria use Type I? give an example of an organism which uses both types.

They are highly conserved in organisms because all photosynthetic organisms contain them; these include organisms such as purple bacteria, which are very ancient and were amongst the first photosynthetic organisms to exist.

Green sulfur bacteria use type I because it has evolved in high-sulfur environments, and I use iron-sulfur centres as e-carriers.

Plants and algae are examples of organisms which use both types of RC.

what is the main job of PSII and what is the main job of PSI ?

PSII acts as a proton gradient generator = since it splits water into H2 and O

PSI = produces reducing power, from which ATP can be made.

What is 1 PS II made of? What is the difference between this and PS II supercomplex? give reason for why the PSII complex exists

PSII = made of core = which has D1 and D2 proteins intertwined tightly together, forming a very dense core

there are also some other antennas which are closely related to the core D1 and D2 = CP47 and CP42

And there are also two antennas which are peripheral LHCIIs(one strongly bound and the other mildly)

There is also cyt bf 559 which has a heme group attached to it and is a single alpha-helical structure.

• The PSII supercomplex varies since it contains two PSII cores for increased stability since the molecules are very hydrophobic and will stick together.

what are the features of CP47 and CP42 ? and how are they different and how are they similar ?

What are the features of cytbf 559 ? mention what it has attached to it .

• CP47+ CP42 = transmembrane region and soluble region

  The soluble part is made of alpha helices and flexible beta-sheet.

  Contains six transmembrane alpha helices.

  Contains chl a and beta carotene

• differences between CP47 and CP42 = the arrangement of the beta carotenes within the structure differ.

• cut bf-559 = is made of a single alpha-helical structure, which varies across species

  it binds to a single cofactor =heme-b cofactor = this has a similar structure to heme it is made of tetra payroll = it is a perfect e-donor.

  Possible function to defend PSII from oxidative damage.

How do we know that the core complex is a redox network?

mention what is the distance needed for e- transfer.

Because there are pi e-conjugated molecules, and the distances between them are the right ones for energy transfer and e-transfer.

The distance required for the transfer to happen is 10-20 A

What is the special pair ? and what is their main function ?

The special pair is two chl a’s which are very tightly held together, so much that they appear as one when viewed.

Pd1 and Pd2

Their function is to absorb at 680 nm = and transfer that energy on so that eventually water can be split.

This is where the first events of photosynthesis take place in PSII.

in what two sections is the core of PSII split ? mention what is attached to each branch.

A branch and B branch

A branch = PheoD1, ChlZD1, Chl D, D1TyrZ PD1 ALL bound to D1 BESIDES plastoquinone (Qa) and Mn cluster, which is only partially attached to D1 and CP47

B branch = pheoD2, ChlD2, CHlzD1, TyrP, Pd2 AAL bound to D2 BESIDES Qb (platiquinone), heme which is attached to cyt-b559, and the beta carotene, which sometimes is present in the crystal structures and sometimes is not. Hence, it is speculated that it is transiently bound.

What is the function of D1 and D2 tyrosines? What is their name?

• The function is to connect the Mn cluster to the special pair to transfer energy between them.

• They are called TyrZ and TyrD.

• Tyr D on the B branch will not have this function since there is only one Mn cluster, and this is located in the A branch. Hence, the process of TyrD has yet to be fully known.

what is the role of ChlZ D2 and ChlZ D1 ?

they are peripheral but still interact with the antenna, and their function acts as an energetic bridge between the rest of the antenna and the core antenna.

what is interesting about the structure of Pheo A and PheoB ?

their structure is the same as the one of chlorophyll besides the fact that they do not have a central Mg atom.

Why is the OEC on the lumenal side of the membrane? What does it contain? how many Mn atoms ? What is its function? Why does it need to be very coordinated?

OEC is on the lumenal side because it splits water; hence, it needs to be in a soluble protein region to access water.

It comprises 4 Mn clusters, H2O and O2, some transiently bound to it, and some calcium atoms.

Its function is why the biosphere exists, and it splits water into H2, and O. The H2 is then used for the proton gradient whereas the O is a byproduct.

Due to the type of chemical reaction it carries out, it needs to be highly coordinated, hence why several H-bonds with other polar amino acids are holding it into place.