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Biostructures, Energetics and Synthesis > Photosynthesis > Flashcards

Photosynthesis Flashcards

1
Q

What entropy does life require?

A

Negative entropy

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2
Q

What is ∆p?
What does it drive the formation of?

A

∆p – Electrochemical proton gradient/Proton motive force (pmf)

Drives the formation of ATP

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3
Q

Explain the Jagendorf acid-bath experiment
(refer to image on notes)

A

Thylakoids are incubated in a low pH medium in the dark containing a weak permeable acid

The acid will diffuse across the membrane and dissociate inside to equilibrate the pH to 4 inside

It is then rapidly transferred to a high pH medium, and a transient ∆p is created, allowing ATP synthesis if ADP and Pi are added

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4
Q

Give evidence for chemiosmosis (hint: uncoupler)

A

If the proton gradient formed by electron transport is needed to generate ATP, then its abolition should inhibit ATP formation

The proton gradient can be abolished by an un-coupler; A molecule which facilitates diffusion of protons across the normally impermeable membrane
- ATP synthesis was abolished; Electron transport and ATP synthesis were now uncoupled

A light-driven proton pump ‘bacteriorhodopsin’ could, when reconstituted in lipid vesicles with ATP synthase, drive the production of ATP

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5
Q

What are NADH and FADH2 and what happens to them during respiration?

A

They are electron carriers

They are reduced in glycolysis, the link reaction and the citric acid cycle, and then oxidised in the mitochondria to make ATP

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6
Q

What is reductant-powered electron transfer coupled to?
What does this generate?

A

Proton transfer across a membrane

This generates electrochemical proton gradient (∆p)

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7
Q

Where does photosynthetic electron transport occur?
Where does CO2 fixation occur?

A

Thylakoid membrane

Stroma

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8
Q

What does light energy do to electrons when absorbed?
What is done with the free energy that is released?

A

Excites electrons; Raises the redox potential from positive to negative

Free energy released used to generate ∆p for ATP synthesis

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9
Q

What is done with the free energy released when electrons flow from a negative to positive redox potential? (give an example)
What is this called?

A

Free energy released can be used to do work e.g. move protons from an area of low concentration (matrix) to an area of high concentration (MIS)

This is called chemiosmotic coupling

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10
Q

Similarities and Differences of Respiration and Photosynthesis?

A

Both involve electrons being transferred down gradient of redox potential with free energy released used to power formation of ∆p for ATP synthesis

Respiration uses electrons from reductants
Photosynthesis uses electrons energised by light

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11
Q

What is the structure of Chlorophyll? (Similarities with haem?)

A

It formed of 2 parts:
- Tetrapyrrole ring; Similar to haem but it coordinates an Mg2+ ion, not an Fe2+
- Hydrophobic phytyl tail

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12
Q

What system in the tetrapyrrole ring is responsible for light absorption?
What happens when chlorophyll absorbs light?

A

Conjugated pi-electron system

When chlorophyll absorbs light an electron in this region is promoted to a higher energy level

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13
Q

What complexes do light driven reactions occur in?

What do they result in? (hint: electron transfer; by-products?)

A

PSII and PSI

They result in electron transfer via a chain of acceptors from water to NADP+, with oxygen formed as a by-product

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14
Q

How do the reaction centres use light energy?

A

To drive energetically unfavourable reactions (+∆G) that transfer an electron from a donor with a positive redox potential (water) to an acceptor with a more negative redox potential (NADP+) i.e. uphill

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15
Q

+∆G vs -∆G

Is a negative to positive redox potential favourable or unfavourable

A

+∆G - Unfavourable reactions
-∆G - Favourable reactions

Favourable (-∆G)

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16
Q

What is the typical redox potential for acceptors and donors

A

Donors - Negative redox potential
Acceptors - Positive redox potential

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17
Q

What is the structure of a photosystem?

A

Antenna complex is formed of hundreds of chlorophylls which transfer absorbed light energy to the special pair chlorophylls of the reaction centre that are redox active

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18
Q

Why are antenna systems needed?

A

The antenna increases RC excitation rate by 2 orders of magnitude
The antenna acts to capture and concentrate light energy

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19
Q

What does variation in the length of the conjugated pi-electron affect?

A

It affects the wavelengths of light absorbed by each pigment

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20
Q

Why are multiple pigment types combined in the antenna?

A

To broaden the spectral cross-section of light energy that is absorbed and transferred to the reaction centre chlorophylls

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21
Q

How are antenna proteins and pigments linked?
Where does the complex sit and why?

A

Antenna proteins non-covalently bind pigments at high concentrations to ensure efficient light absorption

This complex sits in the membrane and is extremely hydrophobic

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22
Q

How are PSII and Light Harvesting Complex II (LHCII) linked?
How is the system modular?

A

They form a dimeric super complex

Modular system as there is more LHCII when growing under low light, and less LHCII when growing under high light

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23
Q

How are PSI and Light Harvesting Complex I (LHCI) linked?
How is the system modular?

A

They form a monomeric super complex

Modular system as there is more LHCI when growing under low light, and less LHCI when growing under high light

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24
Q

What photons do molecules absorb?

What is fluorescence and which state does it occur from?

A

They only absorb photons with energy equal to the energy gap between electron orbitals

Fluorescence is when photons are re-emitted; This always occurs from the lowest excited state

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25
Q

How many major excited states does chlorophyll have?

Which states do red and blue photons match?

A

Chlorophyll has 2 major excited states

Red photons match the S0->S1 (first excited state) gap
Blue photons have more energy than red photons (shorter wavelength) and so they excite electrons to the S2 state

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26
Q

What happens to an electron excited by a blue photon?

A

Promoted to S2 state

Rapidly loses some energy through vibrational relaxation
Drops to S1 state through internal conversion (heat)
Further vibrational relaxation reduces electrons energy to lowest energy level of the S1 state

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27
Q

What then happens to the photon in the S1 state? (hint: 2 ways)

A

Internal conversion from S1 to S0 occurs, but more slowly than S2 to S1
As it is slower, fluorescence (photon emission) competes as an alternative channel of de-excitation

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28
Q

Why is internal conversion from S1 to S0 slower than that for S2 to S1?

A

S1 to S0 is slower as the electron is closer to the nucleus and so is more stable

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29
Q

What happens to S1 electrons between adjacent chlorophylls?

A

Fluorescence and internal conversion are so slow that FRET can compete

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30
Q

What is FRET?

A

Forster Resonance Energy Transfer

This occurs if 2 chlorophylls are in close proximity, with excited state energy levels that overlap
Essentially transfers excitation energy from an electron on one chlorophyll to another

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31
Q

What is resonance?

A

When the donor emission and acceptor absorption spectra overlap, FRET can occur between them in a distance (R0) dependent fashion

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32
Q

Explain FRET efficiency (hint: distance)

A

The efficiency of FRET varies with the 6th power of the distance

i.e. If the distance between 2 molecules doubles, the FRET transfer time increases by 64 times
FRET is only efficient over short distances (<7nm)

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33
Q

How is each pigment binding site in LHCII different?
Effect of this? (hint: spectra and flow)

A

They all vary in there excited state properties:
- Energy
- Spectra
- Excited state lifetime

This diversity in binding sites energies broadens spectral cross-section further and creates directionality in energy flow

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34
Q

How is directionality achieved through the range of binding sites?
What happens in the RC?

A

Chlorophylls closer to the reaction centre (RC) have excited state at lower energies than those further out in the antenna

So excitation energy cascades downhill towards the RC by FRET, where it is ‘trapped’ as an electron transfer reaction

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35
Q

Name for special pair in PSII?

A

P680

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36
Q

What redox reactions is PSII involved in?

A

Oxidising H2O to O2
Reducing PQ to PQH2

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37
Q

Equation for energy of 1 mole of photons?
Meaning of each term?

A

ΔG = (Nhc)/wavelength of light

N - Avogadro’s number
h - Planck’s constant
c - Speed of light in vacuum

38
Q

∆E0’ equation?

A

∆E0’ = E0’(acceptor) – E0’(donor)

39
Q

What co-factor is key for PSII electron transfer?

A

Manganese cluster

40
Q

How many turnovers of PSII electron transfer is required for 1 PQH2?
How many for 1 O2?

A

2 turnovers for 1 PQH2
4 turnovers for 1 O2

41
Q

Process of PSII electron transfer reactions
(refer to images on notes)
What branch(es) does charge separation occur down in PSII?

A

Just down branch A

42
Q

What happens to electrons in chlorophyll when excited?
What does the Mg2+ ion do?

A

Upon excitation, the electron is lost from the tetrapyrrole ring in the RC chlorophyll rather than from the Mg2+ ion which is redox inactive

The resulting hole/electron is delocalised over the tetrapyrrole ring

In chlorophyll the Mg2+ ion tunes the absorption spectrum of the molecule and provides a coordination site for interaction with protein

43
Q

FRET between antenna and RC; Which direction?

A

FRET only occurs from antenna to RC
No transfer from RC to antenna

44
Q

How is plastoquinone converted to plastoquinol?
What happens after the conversion?

A

2 e- reduce the 2 C=O carbons on plastoquinone from +2 to +1 oxidation state, forming 2 OH-
2 H+ are taken up from the stroma to form plastoquinol

Once PQH2 is formed at the QB site, it is exchanged for PQ

45
Q

How is the manganese cluster changed and then restored to its original state?

A

Manganese ions in the cluster are progressively oxidised

It is restored to its original state by electrons from H2O

46
Q

How is charge separation stabilised?

A

A chain of electron acceptors energetically ‘downhill’ from P680* ensures e- and hole (+) are rapidly separated spatially

47
Q

2 key molecules in PSI?
What enzyme catalyses their reaction? (hint: tells us which is reduced)

A

Ferredoxin and Plastocyanin

Ferredoxin Oxidoreductase

48
Q

Which molecule is oxidised and which is reduced by PSI?

A

PSI oxidises plastocyanin and reduces ferredoxin

49
Q

Name for special pair in PSI?
What branch(es) does charge separation occur down in PSI?

A

P700

Branch A or B

50
Q

Process of electron transfer in PSI
(see image on notes)

A
51
Q

How is the electron hole filled in PSI?

A

P700+ is re-reduced by an e- from plastocyanin

52
Q

What are Ferredoxin and Plastocyanin?

A

They are both small soluble electron transfer proteins

53
Q

Key feature of Plastocyanin? (hint: ion)
What happens to this feature? (hint: Cb6f)

A

A copper ion is bound at its active site; This acts as the electron carrier
The copper ion is oxidised from Cu+ to Cu2+ by PSI, and reduced back by cytochrome b6f

54
Q

What does Ferredoxin bind at its active site?

A

Binds a 2Fe-2S cluster at its active site that acts as the electron carrier

55
Q

What does Marcus theory say about the rate of ET reaction and direct charge recombination?

A

ET reaction rate decreases in the ‘inverted region’ as large driving forces between redox couples slows ET rates

Charge recombination falls in the inverted region and a slow ET rate
- More likely for electron to travel along a branch than recombine with the hole

56
Q

Structure of Cytochrome b6f?
What does it bind per monomer?

A

Dimer

  • 2 x PQ
  • 1 x carotenoid
  • 1 x chlorophyll
  • 4 x haems
  • 1 x 2Fe2S cluster
57
Q

Co-factors in cytochrome b6f?
What are they linked to?
What cluster is at the centre and what is it coordinated by?

A

2 c-type haems
2 b-type haems

c-type haems are linked to protein
b-type haems are linked to central Fe ion

Iron-sulphur cluster (2Fe2S)
Coordinated by histidine and cysteine

58
Q

Process of bifurcated electron transfer (2 steps) (hint: how Cu2+ is reduced)
(see images on notes)

A

Step 1:
- PQH2 is oxidised
- 2 protons are deposited into the lumen and the 2 electrons follow different paths (bifurcate)
- 1 electron reduces Pc, and 1 electron is stored in haem cn

Step 2:
- Another PQH2 is oxidised
- 2 protons are again deposited into the lumen and the 2 electrons follow different paths (bifurcate)
- 1 electron reduces a second Pc, and 2 electrons reduce the PQ molecule to PQ-2, which binds 2 protons from stroma to become PQH2

59
Q

What happens during the proton motive Q-cycle? (hint: recycling)

A

Recycling of 1 of the 2 electrons from each PQH2, doubles the number of protons transferred by the complex per PQH2 oxidised, boosting its contribution to the proton motive force (∆p)

60
Q

What does NADP+ reduction by FNR require?
What molecule has this function? (hint: storage)

A

Requires 2 electrons and 1 proton and a place to store 1 electron from ferredoxin, while the FNR waits for the second to arrive

Flavin Adenine Dinucleotide (FAD) of FNR has this function

60
Q

What complex is the ‘end of the line’ for photosynthetic electron?
What happens here?

A

Ferredoxin-NADP+ reductase (FNR)

NADP+ is reduced to NADPH

61
Q

The calvin cycle requires 1.5ATP per NADPH, but only 1.28 ATPs are formed per NADPH in a chloroplast
How is the imbalance in ATP/NADPH ratio corrected?

A

Cyclic electron transport

62
Q

What does cyclic electron transport involve? (hint: returning electrons)
What complex is involved in this pathway? (what enzyme does this act as?)
How does it contribute to ATP formation and correct the imbalance?

A

Involves returning electrons from Ferredoxin to the PQ pool

Photosynthetic complex I; Acts as ferredoxin-plastoquinone reductase

Contributes to pmf, and therefore ATP formation; No NADPH synthesis

63
Q

What enzyme does photosynthetic complex I act as?
What do the 4Fe4S clusters do?

A

Ferredoxin-plastoquinone reductase
The 4Fe4S clusters shuttle electrons from Fd to PQ to make PQH2

64
Q

What is done with the free energy released in the PQ -> PQH2 reaction?

A

Powers movement of 4H+ across membrane; Contributes to pmf

65
Q

Parts of ATP synthase in F-type ATP synthesis?

A

F1 rotor is where ADP+Pi -> ATP occurs
Clamp holds 2 parts of the enzyme together

66
Q

Sets of subunits of ATP synthase (5 sets)

A

a-subunit
c-subunit
γ-subunit
α and β subunits
b2 and δ subunits

67
Q

What do the a and c subunits do?

A

a-subunit - Half channels; Lets protons in on one side, and out on the other side

c-subunit - Proton binding subunits; Number of c subunits varies

68
Q

What does the γ-subunit do? (2 functions)

A

Central stalk that transmits the torque from the c-subunit to the head part of the protein
Also cycles β-subunit between open, loose and tight states

69
Q

What do α and β, and b2 and δ subunits do? (hint: α and β have different functions but link)

A

α and β subunits - 3 of each form the F1 head
- β are catalytically active; α has a structural role, and helps β form the binding site for ADP, Pi and ATP

b2 and δ subunits - Form the ‘clamp’, bridging the F1 and F0 domains, ensuring the 2 parts stay coupled

70
Q

How do protons bind to c-subunits?
What happens in a hydrophobic environment? (hint: pKa)

A

Each c-subunit has a glutamate residue with a carboxy group (negative) to bind protons

In hydrophobic environment, the pKa for the carboxy group is high; This means the group will be protonated at a more basic pH

(low pKa means it is protonated at a more acidic pH)

71
Q

What residues are present on the a-subunit?
What groups do they have and what do they bind?

A

Arginine residues are present, which can bind protons with an amine group

72
Q

What happens when glutamate and arginine residues are in close proximity? (hint: COO- and pKa)

A

COO- is stabilised by the positive charge of arginine
This causes the carboxy groups pKa to drop and become deprotonated and the proton exits the half channel

73
Q

What happens to deprotonated glutamate? (hint: its on side of high H+ conc.)
What does this cause to happen and why?

A

Deprotonated glutamate has low pKa and is on side of high H+, so it can still be protonated

The protonation causes the c-ring to rotate due to the attraction between the positive arginine and the negative glutamate

74
Q

What happens when the γ-subunit rotates?
What are the 3 states?

A

β-subunit conformation changes between 3 states
- O state
- L state
- T state

75
Q

What happens during the 3 states? (hint: involves ATP, ADP and Pi)

A

O state - ATP released
L state - ADP + Pi is bound
T state - ADP + Pi is converted to ATP

76
Q

How many ATP from one c-ring rotation?
How many protons required for one complete rotation of γ-subunit?

A

3 ATP per c-ring rotation

1 proton required for every c-subunit there is, to then produce a γ-subunit

77
Q

With the same pmf, would a smaller or larger c-ring be faster at ATP synthesis?

A

Faster with smaller c-ring

78
Q

With different pmfs, would it be easier to produce ATP with a smaller or larger c-ring?
Why?

A

Easier to produce ATP with a larger c-ring
This is because it requires less pmf to do the same work compared to a smaller c-ring

The larger the c-ring, the larger the pmf multiplier

79
Q

Summary: Out of a smaller or larger c-ring, which is more optimised for rapid synthesis, and which is more optimised for low energy inputs
What do they both sacrifice?

A

Smaller ring is optimised for rapid synthesis sacrificing efficiency
Larger ring is optimised for low energy inputs, sacrificing speed

80
Q

Is ATP synthase reversible?
What does the direction depend on?

A

It is reversible

The direction depends on thermodynamic balance between ∆p and ∆G-ATP

81
Q

What are the 3 parts of the calvin cycle?

A

Carboxylation
Reduction
Regeneration

82
Q

How many molecules of ATP and NADPH are required to reduce 3 CO2, for every complete turn of the cycle?
How many molecules of glycerdaldehyde-3-phosphate are produced?

A

9 ATP
6 NADPH
6 glyceraldehyde-3-phosphate is produced

83
Q

What occurs during carboxylation?
Enzymes involved in catalysis?

A

CO2 is combined with ribulose-1,5-bisphosphate; Catalysed by RuBisCO
Forms an unstable 6 carbon intermediate that splits into 2 molecules of 3-phosphoglycerate

84
Q

Characteristics of RuBisCO?
Subunits? (2 types)

A

Slow enzyme
Low affinity for CO2

High concentrations are needed to match potential supply of ATP and NADPH

8 large catalytic and 8 small regulatory subunits

85
Q

What occurs during reduction? (2 steps)
What is the end product and its major fate?

A

First step involves 3-phosphoglycerate is phosphorylated to form 1,3-bisphosphoglycerate using ATP from light reactions

The second step involves reduction of 1,3bisphosphoglycerate using NADPH to form glyceraldehyde 3-phosphate (GAP)

GAP is the output and is used in sucrose synthesis

86
Q

What occurs during regeneration?
How many molecules of GAP per ribulose-1,5-bisphosphate and CO2?
What is done with the majority of GAP?
Final step?

A

6 GAP for every:
- 3 ribulose-1,5-bisphosphate
- 3 CO2

5/6 GAP molecules are used to regenerate ribulose 5-bisphosphate

Ribulose 5-phosphate is phosphorylated into ribulose 1,5-bisphosphate using ATP from light reactions

87
Q

How does the activity of the light reactions link to and regulate dark reaction enzymes? (2 ways) (hint: thioredoxin and ∆p)

A

∆p is formed across the thylakoid membrane
This increases the pH and the [Mg2+] in the stroma
- H+ influx into the lumen is balanced by Mg2+ efflux to the stroma

Ferredoxin and NADP+ are reduced, changing redox state of the stroma, which is sensed by the thioredoxin
Thioredoxin regulates several calvin cycle enzymes

88
Q

How is RuBisCO regulated? (hint: light reactions)

A

RuBisCO active site contains a lysine which reacts with CO2 to form a carbamate anion that can bind to Mg2+
Mg2+ is provided by the light reactions
Mg2+ is essential for the RuBisCO to function as it activates ribulose 1,5-bisphosphate

89
Q
A

Biostructures, Energetics and Synthesis (2 decks)

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