Johnson (Photosynthesis) Flashcards
(135 cards)
1
Q
How does photosynthesis power biosphere?
A
- source of all food, O and most energy (≈88%)
2
Q
How did photosynthesis change the world?
A
increase in atmospheric O2 conc allowed multicellular organisms to appear
- spike in [O2] is coniferous period
- many trees etc. died and prod fossil fuels present today
- at this time plants also dev lignin in cell walls
3
Q
Why is ps the basis of food chain?
A
- virtually all life depends on it to provide energy in form of red C molecules
4
Q
What are the types of photosynthetic organism, and eg.s?
A
- euk oxygenic ps (chloroplasts) = eg. plants, mosses
- prok oxygenic ps = eg. cyanobacteria (-)
- prok anoxygenic ps = eg. purple bacteria (-)
- archaeal ps = halobacteria
5
Q
Where does photosynthesis take place in euks?
A
- chloroplast thylakoid membrane
6
Q
How is thylakoid membrane specialised for photosynthesis?
A
- highly folded
- providing huge area for light absorption and e- transport
7
Q
How does oxygenic photosynthesis occur in plants?
A
- e- transport in thylakoid membrane
- enzymatic machinery responsible for CO2 fixation located in stroma
- main aldehyde product is glyceraldehyde-3-phosphate
- light and ‘dark’ reactions
8
Q
Are dark reactions really in the dark?
A
- no, only occur in light
- ie, don’t cont if remove light after ATP and NADPH formed
9
Q
What is the photosynthetic e- transfer (PET) chain?
A
- 2 light driven reactions in chlorophyll-protein complexes PSII and PSI
- result in e- transfer via chain of acceptors from water to NADP+, w/ O formed as by product
- e- transfer coupled to pmf formation for ATP synthesis
- none of complexes pump protons, all translocate
- NADPH/NADP+ has v -ve redox pot and H2O/O2 v +ve
- H+ released into lumen
10
Q
What does it mean to say complexes translocate protons instead of pumping them?
A
- get net redistribution by performing reactions on both sides of membrane
11
Q
What is the function of photosystems?
A
- carry out light dep e- transfer
12
Q
What is the structure of photosystems?
A
2 parts:
- reaction centre = where photochemical redox reactions take place
- light harvesting antenna system = responsible for light absorption and transfer of captured light energy to reaction centre
13
Q
What is the key light absorbing pigment molecule in both structures of photosystems, and how is it bound?
A
- chlorophyll
- non covalently bound to these proteins
14
Q
What is the basic structure of photosystems?
A
- antenna complex formed of 100s of chlorophylls
- transfer absorbed light energy to special pair chlorophylls of reaction centre that are redox active
15
Q
What do antenna chlorophylls transfer?
A
- energy, NOT e-s
16
Q
What 2 parts is chlorophyll formed of?
A
- tetrapyrrole ring = similar to haem, but coords Mg2+
- hydrophobic phytyl tail region
17
Q
What is the conjugated π e- system in tetrapyrrole ring of chlorophyll responsible for?
A
- light absorption
- when chlorophyll absorbs light, e- in this region promoted to higher energy level
18
Q
What occurs in the reaction centre chlorophyll molecules, and how does this vary between PSI and PSII?
A
- 1° donor oxidised upon excitation
- -> P680 for PSII
- -> P700 for PSI
- e- transferred to acceptor, which is red
- -> lipid soluble plastoquinone for PSII
- -> soluble protein ferredoxin for PSI
- 1°donor re-red by 2°donor
- -> H2O for PSII
- -> plastocyanin for PSI
19
Q
What is the redox ‘Z-scheme’ for photosynthesis?
A
- light energy used by reaction centres to drive +ΔG reactions that transfer e-s from donor w/ +ve redox pot (water) to acceptor w/ more -ve redox pot (NADP+)
20
Q
What occurs in PSII?
A
- uses light energy to transfer e-s from special pair P680 to lipid soluble PQ
- P680+ drives splitting of water into e-, H+ and O2 (photolysis) by Mn cluster attached to PSII
- protons released into lumen, while 2e-s used to red P680+ to P680
- once red, PQ binds 2H+ from stroma side of membrane
21
Q
What is the overall reaction in PSII?
A
- H2O + PQ + 2H+stroma –> 1/O2 + PQH2 + 2H+lumen
22
Q
What occurs in cytochrome b6f?
A
- similar to complex III in mito
- carries out Q cycle
23
Q
What is the Q cycle?
A
- complex series of reactions that ox PQ and transfer e- to plastocyanin, a small soluble e- transfer protein located on lumen side of thylakoid membrane
24
Q
What is the overall Q cycle reaction?
A
- PQH2 + 2PCox + 2H+stroma –> 2PCred + 4H+lumen
25
What occurs in PSI?
- uses light energy to transfer e-s from special pair P700 to ferredoxin
- P700+ drives ox of plastocyanin (PC) on lumen side of membrane regen P700
26
What is ferredoxin?
- small soluble protein on stroma side of thylakoid membrane
27
What is the overall reaction is PSI?
- PCred + Fdox ----light---> PCox + Fdred
28
What is plastocyanin?
- small soluble e- transfer protein
29
What is the role of plastocyanin?
- Cu ion bound at active site coord by several His residues and acts as e- carrier
- Cu ox from Cu+ --> Cu2+ by PSI and red back to cytochrome b6f
30
What is the role of ferredoxin?
- binds 2Fe-2S cluster at active site
| - bound by several Cys residues that act as e- carrier
31
What occurs in ferredoxin-NADP+ reductase?
- contains FAD cofactor which sequentially ox 2 molecules of Fd
- then uses e-s to red NADP+ --> NADPH, w/ H+ taken up from stroma
32
What is the overall reaction in ferredoxin-NADP+ reductase?
- 2Fdred + NADP + H+stroma --> 2Fdox + NADPH
33
Are the structures of chloro and mito ATPases similar?
- v similar
34
What is the difference between chloro and mito ATPases?
- stoichiometry of H+ of ATP much higher in chloro
| - 14 c subunits, instead of 8
35
What is the overall reaction in CF1CF0 ATPase?
- 14H+lumen + 3Pi + 3ADP --> 14H+stroma + 3ATP + 3H2O
36
What is the meaning of Jablonski diagrams?
- molecules only absorb photons w/ energy equal to energy gap between e- orbitals
37
What are the diff excitation states in Jablonski diagrams?
- S0 = ground state
- S1 = 1st excited state
- S2 = 2nd excited state
38
How do red and blue photons vary in terms of Jablonski diagrams?
- red photons match S0 -> S1 energy gap
- blue photons match S0 -> S2 energy gap
- red are higher energy photons w/ lower wavelength
39
What timescale does light absorption occur on?
- femtosecond (10^-15)
40
What do electronic, vibrational and rotational energy levels show?
- some energy levels more favourable
41
Does photosynthesis need green light, and why?
- yes, underneath leaf
| - as chloroplasts filter out all blue and red light, so green req
42
What is the fate of S2 excited state, and timescale?
- e- v rapidly loses part of absorbed energy as heat internal conversion
- falls to S1 state
- picosecond timescale (10^-12)
43
What are fates of S1 excited state, and timescales?
- slower, nanosecond (10^-9), process as closer to nucleus so lower energy and excited state more stable
- internal conversion to S0 slow enough that fluorescence can compete as alt channel of de-excitation
- if another chlorophyll in close prox then FRET
44
How does energy transfer occur between chlorophylls, and when can this happen?
- FRET
- excited energy transferred from excited donor chlorophyll to acceptor chlorophyll in ground state
- can occur when 2 chlorophylls in close prox and have overlapping excited state energy levels
- keep flipping around and energy cascades between them
45
How is FRET distance dep?
- efficiency varies w/ 6th power of distance
- ie, if distance between donor and acceptor doubles, FRET transfer time increases 64x
- ∴ only efficient over short distances
46
Why are antenna needed?
- increase reaction centre rate by 2 orders of magnitude
| - acts to capture and concentrate light energy
47
What features should antenna have?
- high as poss pigment conc
- wide spectral cross section (as many colours as poss)
- wide spatial cross section
- modularity build up in low light, red in high light (don't need as many antenna complexes in high light as more excitation)
- provide directionality to energy transfer
- min losses of excitation energy to heat and fluorescence, and prevent e- transfer
48
Why is there a pigment variety in plants?
- variation in length of conjugated π e- system affects wavelength of light absorbed by each pigment
49
What is the pigment absorption spectra?
- combo of multiple pigment types in antenna broadens spectral cross section of light energy that is absorbed and transferred to RC chlorophylls
50
What pigments are bound to antenna proteins, and how?
- antenna proteins non covalently bind pigments at v high conc to ensure efficient light absorption
- LHCII 1 of most abundant membrane proteins
51
What is the antenna structure of PSII?
- multiple antenna proteins provide large spatial cross section for light absorption
- ≈ 157 chlorophylls/RC
- PSII forms dimeric supercomplex = 1x LHCII trimer per RC, 2x PSII, 2x LHCII monomers per RC and O evolving complex (catalyst)
52
What is the antenna complex of PSI?
- generally don't have dimers
- multiple antenna proteins provide large spatial cross section for light absorption
- ≈155 chlorophylls/RC
- PSI RC and 4 x LHCI monomers per RC
53
What makes the structure of antenna modular?
- can build up or down
54
What is the modular structure of antenna?
- leaves --> thylakoid membranes --> solubilisation of membranes in detergent --> separation of sucrose grad ultracentrifugation
- [LHCII] increases in low light and decreases in high light
55
What makes each pigment binding site of LHCII unique?
- env of each pigment affects π e- system
| - so pigments excited state properties inc energy, spectra and excited state lifetime
56
What does excited state lifetime mean?
- how long excited state lasts before returning to ground state by photon emission
57
What is the effect of binding site heterogeneity in LHCII?
- range of binding site energies further broadens spectral cross section and creates directionality in energy flow
58
How does the range of site energies provide directionality?
- chlorophylls closer to RC have excited state at lower energies than those further out in antenna
- so excitation energy cascades downhill towards RC by FRET
- where its trapped as e- transfer reactions
59
How is FRET demands balanced w/ ET for stopping LHCs becoming RCs?
- antenna proteins like LHCII evolved to keep far enough apart to avoid raped e- transfer, but close enough to allow FRET
- RCs behave as 1 pigment --> req overlap of mol wavelengths
60
How do you calc energy light contains?
- ΔG = (Nhc) / λ
- N = avogadro's constant
- h = constant
- c = speed of light in vacuum
- λ = wavelength of light
61
PSII is the only biological enzyme known capable of doing what?
- ox H2O to O2
62
How does PSII prevent e-s going astray?
- e- transfer efficiency decays exponentially w/ distance
- RCs evolved to allow FRET from antenna to RC, but no e- transfer from RC to antenna
- gap in middle of protein separates RC from bulk reaction pigments
- isolating RC done by all PS
- don't want so close that e- could go back to antenna complex and cause damage in oxidative reactions
- but close enough to transfer excitation energy = few nms
63
Why are e-s lost from tetrapyrrole ring in RC chlorophyll?
- upon excitation e- lost rather than from Mg2+, which is redox active
64
What is the result of e-s being lost from tetrapyrrole ring?
- resulting hole/e- delocalised over ring
- this is key diff from haem cofactors found in cytochromes where Fe2+ redox active instead
- in chlorophyll Mg2+ tunes absorption spectrum of molecule and provides coord site for interaction w/ protein
65
What provides the free energy input for PSII reaction?
- 4x 680nm photons
66
What are the 2 branches in PSII RC, and in which does e- transfer occur?
- a and b
| - e- transfer only down a, b is 'ghost' branch
67
Why does PSII want to separate e-s spatially and energetically?
- prevent recombination
68
What happens if e- recombines in PSII redox scheme?
- energy lost as heat
69
What happens in the redox scheme of PSII?
- to achieve photolysis redox pot of over +820mV req
- P680+/P680 is high enough to act as oxidants of H2O/O2
- P680 left w/ really +ve charge so can rip e- out of anything
- rips e- out of Tyr as closest residue
- e- ripped out of water bound to Mn cluster by Tyr
70
What is the result of photochemical reaction of PSII RC?
- 2e-s end up on QB
- QB binds 2H+ from stroma and leaves binding site as QH2
- hole does work and is transferred in direction of water and Mn cluster
- e-s transferred to plastoquinone to make plastoquinol (2e- carrier so red twice)
- 2 charge separations driven by 2 photons
- need 4 turnovers to make 1 O molecule
71
What is pheophytin?
- chlorophyll molecule w/ 2H+ instead of Mg2+ at centre
72
What are the starting and final reactions in cascade of photochemical reactions of PSII RC?
- P680 excited (P680*) and cascades along series
| - e- transferred until Y2+ receives from Mn cluster and cycle repeats
73
What is plastoquinone, and what is its role?
- lipid soluble e- carrier
- 2e-s used to red 2 C=O C atoms from +2 to +1, forming 2 OH groups
- 2 H+ req taken up from stroma, once PQH2 formed at QB site its exchanged for PQ from membrane pool
74
How is charge separation stabilised (PSI and PSII)?
- chain of closely packed e- acceptors energetically 'downhill' from P680* ensures e- and hole rapidly separated
- reverse reactions uphill so slow
- 60% loss of energy necessary price of stabilising charge separation
75
What is the 'hole'?
- +ve charge
76
How is water oxidation catalysed by Mn cluster?
- PSII binds Mn cluster
| - P680+ provides thermodynamic driving force for water ox
77
What is the structure of Mn cluster?
- 4 Mn ions and Ca2+ bridged together by O atoms
| - 2 water molecules bound
78
Why can Mn cluster give lots of e-s away?
- can exist in multiple ox states from +2 to +5
79
What occurs during the water oxidation (S state cycle)?
- 4 light driven turnovers of P680 drive evo of 1 O2
- Mn ions progressively oxidised to provide e-s, released from cluster and used to red P680+
- e-s restored by water in final step that sees O=O bond formation, returning catalyst to original state
- protons released deposited into lumen and contribute to pmf
80
How does cytochrome b6f differ from cytochrome bc1 in mito?
- v similar
| - haem c replaced by haem f
81
How is no. of H+ translocated by PSI doubled?
- recycling 1 of 2 e-s from each plastoquinone via low pot chain
82
What does PSI function as?
- light dep plastocyanin (lumen) - ferredoxin (stroma) oxidoreductase
83
What is the antenna structure of PSI?
- similar to PSII
- multiple antenna proteins provide large spatial cross section for light absorption
- ≈155 chlorophylls/RC
- PSI RC and 4x LHCI monomers per RC
84
What is ox and red in PSI reaction?
- ox plastocyanin
- red ferredoxin
- 1 e- transfer
85
What are the pigments of PSI, and their roles?
- binds several key cofactors which take part in e- transfer reactions
- a and b branches active
- unlike PSII quinones tightly bound and don't swim away after reaction
- no pheophytin
- e-s passed between FeS clusters, then to Fd
- like PSII separate e- and hole spatially and energetically
86
What is role of Fd?
- powerful reductant
| - can red NADP+ to NADPH and NO3- to NH4+
87
What are the starting and final reactions in cascade of photochemical reactions of PSII RC?
- P700 excited (P700*)
| - P700+ re-red by e- from plastocyanin and cycle begins again
88
How do no. e- gates vary between PSI and PSII?
- PSI has 1
| - PSII has 2
89
Why is b branch switched off in PSII?
- disfavoured by small energy gap between P680 and ChIB and large gap between QB and PheoB
- simultaneously prevents charge separation in b branch and back reaction of P680+QB- via PheoB
90
What is the result of deactivating b branch?
- creates 2 e- gate
- makes sure both e-s end up on QB and not 1 on QA
- ensuring always quinone to accept e-s (avoiding energy losses)
91
Why does photosynthesis work at all?
- in PSI and PSII most energetically favourable reaction appears to be direct recombination of 1° and 2° radical pairs
92
What is the Marcus theory?
* DIAGRAM*
- explains rates of ET reactions where participants don't undergo large structural changes
- prediction is 'inverted reaction' where large driving forces between redox couples drastically slows ET rates
- direct recombination in this region, so rate v slow
- when e- transferred molecules around e- donor/acceptor have to move to accom change or charge = 'reorganisation energy'
- ET rate optimal when driving force ΔG = reorganisation energy
93
What does the Calvin cycle use ATP and NADH for?
- to convert CO2 into carbs
| - regen ADP, Pi and NADP+
94
What are the 3 main parts of Calvin cycle?
- carboxylation
- reduction
- regeneration
95
What does Calvin cycle use/prod for every complete turn?
- 3 CO2 red
- using 9 ATP and 6 NADPH
- net output 1 GAP
96
What are the consequences of the Calvin cycle being so similar to Krebs cycle?
- KC would run in reverse if had enough CO2
| - some bacteria use this instead of Calvin cycle
97
Why is rubisco not that great?
- slow
- relatively low affinity for CO2
- so v high concs needed to match pot supply of ATP and NADPH
98
How many subunits does rubisco have, and what are there functions?
- 8 large catalytic subunits
| - 8 small regulatory subunits
99
What happens during carboxylation in CC?
- ribulose-1,5-bisphosphate --> enediolate intermediate +CO2 ------rubisco---->unstable intermediate +H2O --> 2 3-phosphoglycerate
- H+ prod in 1st step
100
Is carboxylation in CC energetically favourable?
- yes
101
What happens during reduction in CC?
- 3-PGA + ATP --> 1,3-bisphosphoglycerate
cat by phosphoglycerate kinase
- 1,3-bisphosphoglycerate + NADPH --> GAP + NADP+ + Pi
102
How does reduction in CC relate to glycolysis?
- reverse of steps 6 and 7 of glycolysis
103
What is major fate of GAP?
- sucrose synthesis in cyto
104
What is the result of the fact that both reactions of reduction stage run quite close to equilibrium?
- small changes in ATP/ADP able to push reaction in certain direction
- -> sensitive to mass action effects
105
What happens during regeneration in CC?
- ribulose 5-phosphate + ATP --> ribulose 1,5-bisphosphate + ADP
--> cat by phosphoribulose kinase
- for every 3x 5C RuBP and 3x CO3, 6v GAP formed
- 5/6 req to regen RuBP
- involves complex series of reactions that form 3x RuBP:
3C + 3C --> 6C
6C and 3C --> 4C + 5C
4C + 3C --> 7C
7C + 3C --> 5C + 5C
106
Why is GAP important in plants?
- starting point for multiple metabolic pathways that lead to AA, lipid and nt synthesis
107
How do plants sustain metabolism at night, in roots etc.?
- mito as well as chloro which can ox sugar molecules to prod ATP
108
What is the role of phloem and xylem?
- phloem transports water
| - xylem transports sucrose
109
What makes sucrose more stable?
- bond making it disaccharide of glucose and fructose
110
What is the fate of 1 GAP not used in regeneration in CC?
- exported into chloro in exchange for Pi from cyto
- using translocator protein in chloroplast IM
- converted into 2 types of 6C sugars = glucose-1-phosphate and fructose-6-phosphate
- alt GAP can be converted to glucose-1-phosphate in stroma, then polymerised into starch for storage
111
How are light and dark reactions linked?
- many enzymes of CC also involved in glycolysis or PPP --> so must be carefully reg to avoid futile cycling
- reg achieved by light reactions, mod env of dark reactions
- pmf formation increases pH and [Mg2+] in stroma
112
Why is changing concs when running out of light not an option?
- plants can't store light
| - reactions can start to run in reverse
113
What is the role of thioredoxin?
- regulatory protein
- senses change in redox state of stroma, caused by red Fd and NADP+
- reg activity of several CC enzymes, ensuring activity of light and dark reactions closely coord
114
How is rubisco reg by light and dark reactions?
- active site contains Lys, reacts w/ CO2 to form carbamate anion, then able to bind Mg2+
- both Mg2+ and alkaline conditions req for carbamate formation provided by light reactions
- Mg2+ activates RuBP so readily reacts w/ CO2
115
What is essential for catalytic function of rubisco?
- Mg2+
116
What happens if chloros incubated in low pH medium, then rapidly transferred to high pH medium, and what is this proof of?
- ATP rapidly formed when ADP+Pi added, even in absence of light
- Mitchells' chemiosmotic theory
117
What is virtually all pmf stored as in chloros?
- ΔpH
118
How can Δp and ΔμH+ be interconverted using Faraday's constant?
- ΔμH+ = -FΔp
| - Δp = -ΔμH+ / F
119
How is Δψ dissipated by counterion movements?
- counterions move via VG cation and anion channels in thylakoid membranes
- allows ΔpH to build up
120
Why doesn't ΔpH really affect chloros?
- lumen doesn't contain many enzymes
121
Can no. c-subunits vary in CF1CF0 ATPase?
- varies from structure resolved by atomic force microscopy
122
How does c-ring size vary in CF1CF0 ATPase?
- larger
123
How does Δp relate to ΔGp?
- larger the Δp, the fewer mol H+ spent per mol ATP, so fewer c-subunits req per ATPase
- smaller pmf req larger force multiplier
124
What ratio of ATP:NADPH is req by CC?
- 1.5ATP:NADPH
125
How many ATPs formed per NADPH in photosynthesis, and why is this an imbalance?
- 1.28
- CC req 1.5 ATP per NADPH
- imbalance must be corrected for efficient functioning of ps
- energy balance attained by 2nd type of e- transport taking place in chloroplasts, cyclic e- transport, that prod only ATP
126
What is the role of cyclic e- transport (CET) chain in plants?
- gen ATP, but no NADPH
- so rebalances ATP/NADPH ratio
- protein PGRL1 acts as ferredoxin-plastoquinone oxidoreductase
- alt pathway of CET may involve chloro NADPH-plastoquinone oxidoreductase (NDH-1), similar to mito complex I
127
How does membrane folding divide CET form LET?
- thylakoid membranes divided roughly 80:20 between grana and stroma lamellae thylakoids
- reflects division of labour between CET and LET req to achieve 1.5 ATP/NDPH ratio
128
What is lateral heterogeneity?
- PSII-LHCII residues almost entirely in grana
- PSI-LHCI in 2 pops
- -> 1 in margins of grana that form LET domain w/ cytochrome b6f
- -> 2nd in stromal lamellae w/ cytochrome b6f, forming CET domain
129
What is photorespiration?
- rubisco can cat wasteful competition reaction between RuBP and O2
- phosphoglycerate molecule prod is metabolic 'dead-end', must be converted to CO2
- at 25° rate of carboxylation 4x that of oxygenation (decreases at lower temps)
- photoresp raises req ATP:NADPH ratio
130
How do C4 plants avoid photoresp?
- evolved w/ energy dep CO2 concentrating method = C4 pathway
- assoc w/ special leaf anatomy = Kranz anatomy
131
What are most plants we eat?
- C3
132
Where is photoresp a major cause of inefficient photosynthesis?
- warmer climates
133
How do C3 and C4 plants vary?
- C4 have bundle sheath of cells surrounding central vein w/in leaf, which in turn are surrounded by mesophyll cells
134
What occurs during the C4 pathway?
- mesophyll cells fix CO2 into malate
- malate exported to bundle sheath cells
- decarboxylated to pyruvate
- regen NADPH and CO2
- mesophyll cells don't have enzymatic machinery of CC
- high CO2 conc resulting in bundle sheath allows rubisco to min photoresp
135
How does ATP req for C4 pathway vary from C3, and where does extra ATP come from?
- 15 ATP req for each GAP synthesised (9 in C3)
- extra ATP prod by CET
- C4 costs more but C3 not efficient in tropics
