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Biostructures energetics and synthesis > Johnson > Flashcards

Johnson Flashcards

1
Q

what is Δp

A

pmf

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2
Q

how do uncouplers work with eg

A

they allow the diffusion of protons through a normally impermeable membrane without passing through ATP synthase - dissipating the Δp
eg. Dinitrophenol DNP

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3
Q

what is the proton motive force

A

the potential stored across a biological membrane, established by coupling of electron transfer to proton transfer

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4
Q

what is chemiosmositic coupling

A

electrons traveling from -ive to +ive redox potential releases free energy which can be used to do work
eg. movement of protons from low concentration in the matrix to high concentration in intermembrane space

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5
Q

what is excitation in photosynthesis

A

light energy is used to increase electrons from a more positive to a more negative redox potential

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6
Q

what is the structure of a chlorophyll molecule

A

a tetrapyrrole ring like in haem with a central magnesium (Mg2+) ion instead on iron
it has a conjugated pi system of electrons responsible for light adsorption
hydrophobic phytyl tail

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7
Q

what do PSII and PSI do

A

facilitate electron transfer via a chain of acceptors from water to NADP+.

Electron transfer is coupled to the formation of a proton gradient for ATP synthesis.
Deposition of H+ in the lumen drives pmv for ATP synthase

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8
Q

what is the role of the magnesium ion in chlorophyll

A

to tune the pi electron system for different wavelengths of light

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9
Q

what is redox potential (couple)

A

a measure of how good of a reductant a redox couple is

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10
Q

-ive redox potential

A

good donors of e-

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11
Q

what does a +ive redox potential mean

A

the couple are good acceptors of e-
(easily reduced)

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12
Q

what is the special pair in PSII

A

P680

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13
Q

what is the special pair in PSI

A

p700+/p700

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14
Q

why are the special pairs special

A

they are redox active, able to donate and receive electrons

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15
Q

what is the point of antennas in a PS

A

broad spacial and spectral cross section

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16
Q

similarities of PSII antenna structure and PSI antenna structure

A

both form a super complex with their respective light harvesting complexes (LHCII and LHCI)
both contain chlorophylls and a reaction centre with a special pair
both are modular, built up in low light, down in high light

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17
Q

differences of PSII antenna structure and PSI antenna structure

A

PSII is a dimeric complex, PSI is monomeric
PSII has an oxygen harvesting complex in the lumen (of the thylakoid) PSI does not

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18
Q

how long does it take for e- to get excited

A

femtoseconds

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19
Q

how long does it take for an e- to be emitted

A

nanoseconds

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20
Q

what is vibrational relaxation

A

e- decreases in excitation through the energy level, energy lost as heat

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21
Q

what is internal conversion, how long does it take, where does the energy go

A

S2 –> S1, picoseconds, lost as heat
S1 –> S0, nanoseconds, lost as heat or fluorescence remission - red

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22
Q

what is FRET

A

Förster resonance energy transfer

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23
Q

what is the difference between chlorophyll A and B

A

A has a methyl group where B has an aldehyde group

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24
Q

what time scale is FRET

A

picoseconds

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25
composition of pigments in LHCII
4 x carotenoids 6 x chlorophyll a 8 x chlorophyll b
26
what is the time scale of the final electron transfer (special pair)
picoseconds (outcompetes fluorescence reemission or internal conversion)
27
does the environments of light harvesting complexes do
tune the absorption spectra of the pigments and create directionality to the special pair
28
how many turnovers does it take to make PQH2 in PSII, how many photons is that
2, 2
29
how many turnovers does it take to make O2 in PSII, how many photons is that
4, 4
30
what is an electron hole
a positive charge
31
what is pheophytin
basically a chlorophyll molecule 2 protons instead of the Mg2+
32
what is the other ion in the manganese cluster
Calcium but it is not redox active
33
S0 state
II-III-IV-IV loses a e-
34
S1 state
III-III-IV-IV loses a H+ and e-, 1 PQH2 is made
35
S2 state
III-IV-IV-IV loses a H+ and an e-
36
S3 state
IV-IV-IV-IV loses and e-, 2nd PQH2 is made
37
S4 state
V-IV-IV-IV loses 2H+ and O2, 2H2Os brought in to reform catalyst back to S0 state
38
what is the role of water molecules at PSII
to tell fill electron holes (positive charges) with electrons. by product O2, through manganese cluster catalyst and tyrosine
39
what is the role of the manganese cluster in PSII
a catalyst to lower the kinetic energy barrier for water oxidation
40
what drives the oxidation of water in PSII
thermodynamics p680+/p680 has a redox potential of +1200mV so it is able to oxidise water (+820mV) p680+/p680 is able to oxidise because it is more electro positive
41
why are the photosystem molecules in a horseshoe arrangement
to satisfy the distance requirement of electron transfer, electron transfer decays exponentially with distance
42
what is the structure of cytochrome b6f
a dimer which binds 2 x PQH2, 1 x carotenoid, 1 x chlorophyll, 4 x haems (1 electron carriers) and 1 x 2Fe2S cluster (1 electron carrier)
43
what are the haems in b6f
2 C-type haems - covalently bound to proteins 2 B-type haems - coordinate bond to central Fe
44
where are protons contributed to the lumen
the splitting of water in photosystem II the oxidation of plastoquinol in b6f (4)
45
what happens to electrons from the oxidation of PQH2 in b6f
they bifurcate - one takes the high potential chain and one takes the low potential chain
46
what is b6f
a plastoquinol-plantacyanin oxidoreductase
47
how many ATPs are produced per NADPH in linear electron transport vs how many are needed in the Calvin cycle
1.28 vs 1.5
48
what is the ATP deficit
more ATP is needed for the Calvin cycle than linear electron transfer produces but it must be made with no net NADPH produced - cyclic transfer
49
what happens in the high potential chain in b6f
an e- is used to reduce plastocyanin
50
what happens in the low potential chain in b6f
an e- is used to reduce PQ to PQH2
51
what is cyclic electron transfer
photosynthetic complex I 2Fe2S cluster shuttle e- to reduce PQ to PQH2, this is a negative free energy change which can be coupled to the pumping of H+ across the membrane or PGR5 not understood but links to b6f
52
ATP synthase - a subunit
half channel between proton rich and proton poor sides of the membrane
53
ATP synthase - gamma subunit
central stalk - torque responsible for the 3 different conformations of beta subunit
54
ATP synthase - c subunit
proton binding site, binds to E (glutamate) residue -COO-
55
ATP synthase - b subunit
peripheral stalk
56
ATP synthase - alpha subunit
structural support of ATP catalytic site
57
ATP synthase - beta subunit
catalytically active site of ATP synthesis
58
how does the c-ring spin
R in a-subunit lowers the pKa of E allowing it to be deprotonated attraction of charges causes the spinning of the subunits E is still low pKA but in the high [H+] it is allowed to be reprotonated
59
what is open conformation
ATP is made and is ready to leave
60
what is loose conformation
ADP and PI are ready to form phosphoanhydride bond --> becoming ATP
61
what is tight conformation
ATP is formed
62
what does a larger C ring allow
same work done (ATP produced) with less force (pmf)
63
what organism would have a small c-ring
one with a steady supply of energy and a high energy output eg. chasing a prey
64
what are the 3 parts of the Calvin cycle
carboxylation reduction regeneration
65
what products of the light reactions are transferred to the dark reactions
ATP and NADPH
66
what is NADPH
a 1 proton 2 electron carrier
67
why are high concentrations of Rubisco needed
it has a low affinity for its substrate CO2 50% of total leaf protein
68
what is the role of thioredoxin
a regulatory protein senses the reduction of ferredoxin has two -S which can go to -SH to regulate Calvin cycle enzymes eg. Rubisco -S --> -SH also = active
69
how is Rubisco regulated
lysine residue which is critical for catalysis needs Mg2+, a CO2 and an alkaline environment created by light reactions to make the active form of the enzyme
70
what is the fate of GAP (glyceraldehyde-3-phosphate)
lipid, AA and nucleotide synthesis can go to mitochondrion --> respiration
71
what is the net output of the Calvin cycle
1 GAP (glyceraldehyde-3-phosphate) per 3 CO2s using: 9 ATPs, 6NADPHs
72
what is the first phase of the Calvin cycle
carboxylation three ribulose-1,3-bisphosphate + three CO2 --> six 3-phophoglycerate a proton is removed from ribulose-1,3-bisphosphate forming a CC double bond and leaving it open for nucleophilic attack from CO2 this 6C molecule is unstable so splits into two 3Cs (3-phosphogylcerate)
73
what is the second phase of the Calvin cycle
reduction step 1: six 3-phosphoglycerate + 6ATP --> six 1,3-bisphosophoglycerate this is a acetyl phosphate which is then ready to be reduced to an aldehyde six 1,3-bisphosphoglycerate + 6NADPH --> six gyceraldehyde-3-phosphate + 6NADP+ + 3Pi glyceraldehyde-3-phosphate is GAP = the product of the Calvin cycle and photosynthesis
74
what is the third phase of the Calvin cycle
regeneration (of ribulose-1,5-bisphosphate) step 1 five 3C --> three 5C: glyceraldehyde-3-phosphate --> ribulose-5-phophate + 2PI step 2: phosphorylation: three ribulose-5-phosphate + 3ATP --> three ribulose-1,5-bisphosphate + 3ADP
75
what is responsible for the Calvin cycle required ATP:NADPH ratio of 1.5
the Calvin cycle needs 9 ATPs (6 in reduction step 1, 3 in regeneration step 2) 6 NADPHs (6 in reduction step 2)
76
when/why does FRET occur
close together - FRET efficiency decays at 6th power of the distance because it is faster than the S1 -> S0 internal conversion (nano) FRET = pico
77
what makes absorption spectra different
unique binding sites which AAs more or less AAs
78
how to work out the proton:NADPH of linear ET
6 protons are produced C ring size = 14 3 ATPs produced 14/3 = 4.67 6/4.67 = 1.28
79
PQ and PQH2 in cyclic ET
PQ-->PQH2

Biostructures energetics and synthesis (4 decks)

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