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BIOC2005 - Metabolism > 7 - Photosynthesis > Flashcards

7 - Photosynthesis Flashcards

1
Q

How much carbon is fixed by photosynthesis per year?

A

10^13kg

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2
Q

What does the light reaction produce?

A

ATP and NADPH by photophosphorylation and ETC reduction.

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3
Q

Where does the O2 evolved during photosynthesis come from?

A

It is produced when water is oxidised though photolysis.

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4
Q

Give an overview of the dark reaction.

A

ATP and NADPH from the light reaction are used to reduce CO2 to produce triose phosphates.

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5
Q

Why is UV-Visible light absorbed in photosynthesis?

A

Longer wavelength rays are too low energy and higher energy rays are damaging or filtered out by the atmosphere.

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6
Q

What is the functional group in chlorophyll molecules?

A

A Mg ion complexed in a chlorin ring.

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7
Q

What is attached to the fourth ring in the chlorophyll chlorin?

A

A hydrophobic phytol side chain that allows membrane embedding.

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8
Q

Why is having different pigments with different absorption energies useful for an organism?

A

In crowded environments they can be used to form a niche for the organism, and absorb light not used by the others.

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9
Q

What is oxygenic photosynthesis?

A

The standard method of photosynthesis where water is oxidised to provide the electrons leading to oxygen evolution.

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10
Q

What is anoxygenic photosynthesis?

A

When a substance other than water is used as an electron source, often using double the amount in order to also reduce O2 to water.

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11
Q

What are some common anoxygenic photosynthesis substrates?

A

H2S
H2
Lactate

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12
Q

Give the standard equation for oxygenic photosynthesis.

A

CO2 + H2O → CH2O + O2

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13
Q

Give the standard equation for anoxygenic photosynthesis/

A

CO2 + 2(H2A) → CH2 + H2O + 2A-

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14
Q

What are the properties of purple bacteria?

A

Anaerobes capable of anoxygenic photosynthesis using a variety of reductants (though primary hydrogen sulphide).

Calvin Cycle used, unlike prokaryotes.

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15
Q

What are the properties of green sulphur bacteria?

A

Use sulphur products for anoxygenic photosynthesis.
No Calvin Cycle.
Live in low light environments.

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16
Q

What are the properties of green non-sulphur bacteria?

A

Diverse metabolism - variety of anoxygenic reductants used.

Hydroxyproprionate fixation.

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17
Q

What are the properties of helicobacteria?

A

They are known to be anoxygenic, but are otherwise mysterious.

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18
Q

What are the properties of cyanobacteria?

A

Oxygenic, unlike most prokaryotes.

Marine organisms with

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19
Q

What is the chloroplast an example of?

A

A plastid.

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20
Q

What is the aqueous phase inside the chloroplast called?

A

The stroma.

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21
Q

How are the internal membranes in the chloroplast arranged?

A

Into folded thylakoid membranes called lamellae. These are either unfolded (stromal) or appressed into tight grana (granal lamellae).

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22
Q

How did chloroplases evolve?

A

Through endosymbiosis of cyanobacteria.

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23
Q

How do chloroplasts replicate?

A

Independently of the cell using binary fission, after replicating and translating their genome using enzymes in the stroma.

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24
Q

What other forms can chloroplasts exist in?

A

They can often form from starch-filled amyloplasts which interconvert with proplastids, which in turn interconvert with chloroplasts via pregranal plastids.

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25
Q

What is the difference between a chloroplast and a proplastid?

A

Proplastids do not have proper internal membranes or any pigmentation.

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26
Q

What is the site of all photochemical reactions in photosynthesis?

A

The photosystem reaction centre.

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27
Q

What is the structure of the photosystem?

A

A reaction centre embeddded in a membrane and surrounded in the membrane by protein bound antenna chlorophylls with accessory pigments.

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28
Q

What is the function of the antenna chlorophylls?

A

They capture light and bounce it around by resonance energy transfer to the reaction centre.

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29
Q

What do the accessory pigments do?

A

Interact with the antenna chromophores to ensure they trnasfer the energy to other chlorophylls instead of fluorescing.

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30
Q

What is the timescale of resonance energy transfer?

A

0.2ns

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31
Q

What happens when the exciton reaches the reaction centre chlorophyll?

A

The electron it excites causes a charge separation that stimulates electron flow.

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32
Q

What two photosystems are responsible for anoxygenic photosyntehsis?

A

P870 and P840

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33
Q

What photosynthetic prokaryotes use P870?

A

Purple bacteria.

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34
Q

Which anoxygenic has a higher increase in energy between the excited and ground states?

A

P870

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35
Q

What is the order of components in the P870 photosystem?

A

P870* → Pheophytin → Quinone → Cyt bc1 → Cyt c2 → P870

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36
Q

Which component of the anoxygenic ETCs is responsible for producing the electrochemical gradient?

A

The Cyt bc1 complex.

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37
Q

What does the P870 system not have that the P840 does?

A

An mechanism for producing reduced cofactors.

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38
Q

Describe the pathway of the P840 Describe the pathway of the P840 ETC. ETC.

A

Excited electrons can either be passed through quinone to Cyt bc1 and back to the RC via Cyt c553, or given to ferredoxin for use by Fd:NAD reductase for NADH production.

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39
Q

Which bacteria use the P840 photosystem?

A

Green sulphur bacteria.

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40
Q

What enzyme in P840 is responsible for reduction of NAD+?

A

Fd:NAD Reductase.

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41
Q

What two photosystems are required for oxygenic photosynthesis?

A

P680 (PSII) and P700 (PSI).

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42
Q

Where is the entry point for electrons in the oxygenic photosynthetic system?

A

The O2 evolving complex at PSII.

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43
Q

Briefly describe the electron flow between PSII and PSI.

A

Electrons are sourced at PSII, excited and travel down the ETC to P700, creating an electrochemical gradient.

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44
Q

What pathways can the electrons take out of PSI?

A

Cyclical, travelling down the ETC and back to the PSI RC or to Fd:NADP+ Oxidoreductase.

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45
Q

List the components of the PSII electron transport chain.

A

P680* → Pheo → plastoquinone A → Plastoquinone B → Cyt B6f complex → plastocyanin → P700.

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46
Q

Which protein in the oxygenic ETC is responsible for creating the electrochemical gradient?

A

The Cytochrome b6f complex.

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47
Q

At which component of the PSI ETC can the electron flow down either the cyclical or reducing pathway?

A

At the ferredoxin.

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48
Q

List the componenets of the P700 (PSI) ETC.

A

P700* → Chlorophyll → phylloquinone → Fe-S complex → Fd (branch point)

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49
Q

What enzyme is responsible for the non-cyclic pathway in PSI?

A

Fd:NADP+ Oxidoreductase

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50
Q

What is the structure of the photochemical reaction centre of the oxygen evolving complex?

A

Four manganese ions in varying oxidation states and a Ca++ ion.

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51
Q

What stoichiometric issue is raised at the O2 evolving complex?

A

Each H2O oxidation provides enough electrons for four excitations of the reaction centre.

52
Q

How are electrons stored at the O2 evolving complex?

A

In tyrosine residues within the photosystem complex.

53
Q

What happens to the protons produced by photolysis?

A

They are left in the thylakoid lumen to contribute to the eletrochemical gradient.

54
Q

What is photobleaching?

A

The cooldown period caused by an excitation at a reaction centre.

55
Q

Describe the macrostructure of PSII.

A

Exists as a dimer, but with electron flow only through one side. Loosely binds Plastoquinone near the stroma where it is reduced and dissociates into the membrane.

56
Q

What ETC intermediate exists in a pool within the membrane?

A

Plastoquinone

57
Q

Where do the hydrogens used to reduce plastoquinone come from?

A

The stroma, thus contributing to the electrochemical gradient.

58
Q

How many electrons can plastoquinone carry?

A

Two; PQ → PQH2

59
Q

What does membrane borne plastoquinone pass its electrons too?

A

To Cytochrome b6f complex; one to the Rieske Fe-S group and one to the b electron carriers.

60
Q

What does the Q cycle do?

A

Allows more protons to be pumped into the lumen vectorially by PQ.

61
Q

How does the Q cycle work?

A

One in every two electrons passed to the cyt b6f complex is passed back, each two re-reducing a PQ on the stromal side and oxidising it to the Rieske Fe-S group releasing the protons into the lumen.

62
Q

How many protons are pumped into the lumen by cyt b6f by each pair of electrons?

A

Four.

63
Q

How do electrons exit the Cyt b6f Complex?

A

A single electron is passed to the cyt f subunit where it is used to reduce the copper atom on Plastocyanin.

64
Q

Where is plastocyanin found?

A

Dissolved in the lumen.

65
Q

Where does reduced Plastocyanin transfer the electrons between?

A

The Cyt b6f Complex and PSI.

66
Q

Describe the structure of PSI.

A

Exists in thee domain, two main transmembrane mirror images (subunit A and B) that bind plastocyanin at their join in the lumen and each transmit electrons to the reaction centre and then independently through chlorophyll and phylloquinone to Fe-S chains in subunit C at the stromal join.

67
Q

What is the function of subunit C in PSI?

A

Transferring the excited electrons from PSI to ferredoxin in the stroma.

68
Q

Where is ferredoxin found?

A

In the stroma.

69
Q

Why are the two oxygenic photosystems kept seperate?

A

To prevent exciton larceny.

70
Q

What is exciton larceny?

A

When the photosystems are not separated most of the excitons migrate to P700 due to its lower energy requirements, depriving P680 and hence inhibiting non-cyclical pathway due to lack of electron input.

71
Q

How are the photosynthetic complexes separated?

A

By sequestering some in grana, and others in the non-appressed stromal lamellae.

72
Q

Which photosynthetic complexes are found in the grana?

A

PSII, cyt b6f and light harvesting complex II.

73
Q

Which photosynthetic complexes are found in the stromal lamellae?

A

PSI and ATP synthase.

74
Q

How are grana formed?

A

Light Harvesting Complex II (LHCII) binds to PSII and then extends a domain that binds another part of the membrane together into a fold.

75
Q

How is LHCII regulated?

A

Phosphorylation at a Thr residue by Protein Kinase, causing it to dissociate from PSI and the second membrane, removing the grana fold. It is dephosphorylated by Protein Phosphorylase.

76
Q

What is LHCII regulation used for?

A

More or fewer grana control how active each photosystem is and hence whether the cyclical or non-cyclical pathway is favoured.

77
Q

Which photosystem is more active when the grana are removed and what pathway does this favour?

A

P700, so the non-cyclical pathway is favoured due to lack of electron input from photolysis, so less NADPH is produced.

78
Q

When LHCII is phosphorylated…

A

It is inactive, leading to grana dissociation.

79
Q

What factors affect the activity of protein kinase and protein phosphorylase, and hence the state of thylakoid appression?

A

Light and the reduction state of the various electron carriers.

80
Q

What is the ATP synthase in the thylakoid membrane called?

A

The CF0/CF1 Complex.

81
Q

What light-independent reaction do plants use to fix carbon?

A

The Calvin Cycle.

82
Q

What are the alternative names for the calvin cycle?

A

Calvin-Benson-Bassham Cycle

Photosynthetic Carbon Reduction Cycle

83
Q

What is the product of the Calvin Cycle?

A

3C triose phosphates.

84
Q

How are triose phosphates incorporated into macromolecule anabolism?

A

They are converted to hexose phosphates to make sucrose, cellulose or starch, and on to pentose phosphates for protein, nucleotide and lipid production.

85
Q

What are the three stages of the Calvin Cycle?

A

1 - Fixation
2 - Reduction
3 - Regeneration

86
Q

How many CO2 molecules are fixed per spin of the calvin cycle?

A

One.

87
Q

How many times must the calvin cycle spin to produce a single triose phosphate output?

A

Three, as only one carbon is fixed per cycle.

88
Q

How many ATP and NADPH molecules are required for each spin of the Calvin cycle?

A

3 ATP and 2 NADPH.

89
Q

How many ATP and NADPH molecules are required to produce a single triose phosphate?

A

9 ATP and 6 NADPH.

90
Q

How is it easiest to consider the calvin cycle?

A

With each reaction occurring thrice before the cycle continues.

91
Q

To what molecule is the CO2 added?

A

(5C) Ribulose 1,5 BisPhosphate

92
Q

What reaction is catalysed by Rubisco?

A

The carbon fixation and hydrolysis to two 3C molecules.

93
Q

Describe the unusual features of plant rubisco.

A

Hexadecameric, with some subunits expressed in the chloroplast and some in the nucleus.
Incredibly low turnover number of 3 fixings per second, to compensate for this it is expressed in colossal amounts.

94
Q

What proportion of soluble chloroplast proteins are rubisco?

A

Around half.

95
Q

Explain the nature of rubisco regulation.

A

Normal regulation is not appropriate because of the low turnover number, so absolute ‘on/off’ regulation is used.

96
Q

What protein modification must occur to rubisco before it can be active?

A

Carbamoylation of Lys-201.

97
Q

How is rubisco inhibited?

A

It is inactive without manual stimulation, as although the lys-201 carbamoylation is spontaneous it is far more likely to ineffectually bind ribulose 1,5-BisP before this occurs, concealing the residue that requires activation.

98
Q

How is rubisco activated?

A

Rubisco Activase uses ATP hydrolysis to evacuate the ribulose 1,5-BisP from the un-carbamoylated active site, thus allowing the spontaneous Lys-201 carbomoylation to occur.

99
Q

What regulates the activation of rubisco?

A

The activity of Rubisco Activase is dependent on high light intensity, indicating that the light reaction is active enough to provide for the Calvin Cycle.

100
Q

What 3C molecule is the product of the fixation stage?

A

Glyceraldehyde 3-Phosphate (G3P)

101
Q

What other triose phosphate does G3P exist in equilibrium with? What enzyme is this due to?

A

DHAP, due to presence of Triose Phosphate Isomerase.

102
Q

Which possible fate of the glyceradehyde-3-P occurs solely within the stroma?

A

Combination with a DHAP to produce a fructose sugar, allowing gluconeogenesis to occur for starch production.

103
Q

How do the triose phosphates exit the chloroplast?

A

DHAP leaves through the Pi - Triose Phosphate Antiporter, ensuring that a Pi group enters to replace it.

104
Q

Why must a phosphate group be imported for every DHAP exported?

A

Because DHAP is always shipped from the chloroplast and dephosphorylated, which would otherwise eventually lead to depletion of phosphate in the chloroplast.

105
Q

What are the most common uses of DHAP on immediate exit from the stroma to the cytosol?

A

Interconversion with G3P and entry into either glycolysis or sucrose synthesis.

106
Q

What is the third stage of the Calvin Cycle?

A

Regeneration of ribulose 1,5 Bis-P.

107
Q

What are the substrates used to reproduce ribulose 1,5 bisP in thee regeneration stage?

A

G3P and DHAP, with complex stoichiometry.

108
Q

What classes of enzymes are involved in the regeneration stage of the Calvin Cycle?

A

Aldolases, Transketolases, Phosphatases, Isomerases (Inc. epimerases)

109
Q

How many points of ribulose 1,5 bisP exit are there in the complicated series of reactions in the regeneration stage of the Calvin Cycle?

A

Two.

110
Q

How much ATP/NADPH is consumed at the regeneration stage of the Calvin Cycle?

A

1 ATP per cycle, 3 ATP per TP output.

111
Q

How much ATP/NADPH is consumed at the fixation stage of the Calvin Cycle?

A

2 ATP per cycle, 6 per TP output.

112
Q

How much ATP/NADPH is consumed at the G3P generation stage of the Calvin Cycle?

A

2 NADPH per cycle, six per TP output.

113
Q

What is the regulation of the Calvin Cycle ultimately dependent on?

A

Light intensity.

114
Q

What protein is responsible for the direct regulation of the Calvin Cycle enzymes?

A

Thioredoxin.

115
Q

How is thioredoxin activated?

A

High light intensity means there are many electrons in PSI, and the ferredoxin in the stroma is mostly reduced. A small number of these are used not for NADPH production but by Fd-thioredoxin Reductase to reduce a disulphide bond to two -SH groups.

116
Q

How does thioredoxin regulate Calvin Cycle enzymes?

A

The enzymes also possess conformation changing disulphide bonds, which can in turn be reduced by the thioredoxin to sulphydryl groups that allow the protein to be activated.

117
Q

What happens to the Calvin Cycle regulatory system in the dark?

A

Not enough ferredoxin is reduced to reduce ferredoxin with, and the electrons that have been used to reduce the enzymes are lost over time in the reduction of water.

118
Q

What enzyme is responsible for photorespiration?

A

Rubisco

119
Q

What property of the enzyme allows photorespiration to occur?

A

Lack of specificity for CO2.

120
Q

How is photorespiration thought to have evolved?

A

Rubsico first evolved when the atmosphere contained far less O2, so photorespiraiton was less of an issue. CO2 is also a difficult molecule to be specific for.

121
Q

How often does photorespiration occur compared to carbon fixation?

A

O2 is incorporated by rubisco instead of CO2 every three or four reactions.

122
Q

What are the products of photorespiration, and what are they used for?

A

1x 3-phosphoglycerate, the normal product.

1x 2-phosphoglycolate, a biologically useless product.

123
Q

Why is 2-Phosphoglycolate production a problem?

A

Because it is biologically useless and very energy costly to convert back to 3-Phosphoglycerate.

124
Q

What pathway is used to salvage the 2-Phosphoglycolate?

A

The Glycolate Pathway

125
Q

What three parts of the cell does the glycolate pathway occur in?

A

The chloroplast, the peroxisome and the mitochondria.

126
Q

What gaseous exchange does photorespiration cause?

A

Net production of CO2 from O2 through decarboxylation in the mitochondria.

BIOC2005 - Metabolism (8 decks)

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