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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
Q

composition of pigments in LHCII

A

4 x carotenoids
6 x chlorophyll a
8 x chlorophyll b

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26
Q

what is the time scale of the final electron transfer (special pair)

A

picoseconds (outcompetes fluorescence reemission or internal conversion)

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27
Q

does the environments of light harvesting complexes do

A

tune the absorption spectra of the pigments and create directionality to the special pair

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28
Q

how many turnovers does it take to make PQH2 in PSII, how many photons is that

A

2, 2

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29
Q

how many turnovers does it take to make O2 in PSII, how many photons is that

A

4, 4

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30
Q

what is an electron hole

A

a positive charge

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31
Q

what is pheophytin

A

basically a chlorophyll molecule 2 protons instead of the Mg2+

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32
Q

what is the other ion in the manganese cluster

A

Calcium but it is not redox active

33
Q

S0 state

A

II-III-IV-IV loses a e-

34
Q

S1 state

A

III-III-IV-IV loses a H+ and e-, 1 PQH2 is made

35
Q

S2 state

A

III-IV-IV-IV loses a H+ and an e-

36
Q

S3 state

A

IV-IV-IV-IV loses and e-, 2nd PQH2 is made

37
Q

S4 state

A

V-IV-IV-IV loses 2H+ and O2, 2H2Os brought in to reform catalyst back to S0 state

38
Q

what is the role of water molecules at PSII

A

to tell fill electron holes (positive charges) with electrons. by product O2, through manganese cluster catalyst and tyrosine

39
Q

what is the role of the manganese cluster in PSII

A

a catalyst to lower the kinetic energy barrier for water oxidation

40
Q

what drives the oxidation of water in PSII

A

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
Q

why are the photosystem molecules in a horseshoe arrangement

A

to satisfy the distance requirement of electron transfer, electron transfer decays exponentially with distance

42
Q

what is the structure of cytochrome b6f

A

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
Q

what are the haems in b6f

A

2 C-type haems - covalently bound to proteins
2 B-type haems - coordinate bond to central Fe

44
Q

where are protons contributed to the lumen

A

the splitting of water in photosystem II
the oxidation of plastoquinol in b6f (4)

45
Q

what happens to electrons from the oxidation of PQH2 in b6f

A

they bifurcate - one takes the high potential chain and one takes the low potential chain

46
Q

what is b6f

A

a plastoquinol-plantacyanin oxidoreductase

47
Q

how many ATPs are produced per NADPH in linear electron transport vs how many are needed in the Calvin cycle

A

1.28 vs 1.5

48
Q

what is the ATP deficit

A

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
Q

what happens in the high potential chain in b6f

A

an e- is used to reduce plastocyanin

50
Q

what happens in the low potential chain in b6f

A

an e- is used to reduce PQ to PQH2

51
Q

what is cyclic electron transfer

A

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
Q

ATP synthase - a subunit

A

half channel between proton rich and proton poor sides of the membrane

53
Q

ATP synthase - gamma subunit

A

central stalk - torque
responsible for the 3 different conformations of beta subunit

54
Q

ATP synthase - c subunit

A

proton binding site, binds to E (glutamate) residue -COO-

55
Q

ATP synthase - b subunit

A

peripheral stalk

56
Q

ATP synthase - alpha subunit

A

structural support of ATP catalytic site

57
Q

ATP synthase - beta subunit

A

catalytically active site of ATP synthesis

58
Q

how does the c-ring spin

A

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
Q

what is open conformation

A

ATP is made and is ready to leave

60
Q

what is loose conformation

A

ADP and PI are ready to form phosphoanhydride bond –> becoming ATP

61
Q

what is tight conformation

A

ATP is formed

62
Q

what does a larger C ring allow

A

same work done (ATP produced) with less force (pmf)

63
Q

what organism would have a small c-ring

A

one with a steady supply of energy and a high energy output eg. chasing a prey

64
Q

what are the 3 parts of the Calvin cycle

A

carboxylation
reduction
regeneration

65
Q

what products of the light reactions are transferred to the dark reactions

A

ATP and NADPH

66
Q

what is NADPH

A

a 1 proton 2 electron carrier

67
Q

why are high concentrations of Rubisco needed

A

it has a low affinity for its substrate CO2
50% of total leaf protein

68
Q

what is the role of thioredoxin

A

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
Q

how is Rubisco regulated

A

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
Q

what is the fate of GAP (glyceraldehyde-3-phosphate)

A

lipid, AA and nucleotide synthesis
can go to mitochondrion –> respiration

71
Q

what is the net output of the Calvin cycle

A

1 GAP (glyceraldehyde-3-phosphate) per 3 CO2s
using: 9 ATPs, 6NADPHs

72
Q

what is the first phase of the Calvin cycle

A

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
Q

what is the second phase of the Calvin cycle

A

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
Q

what is the third phase of the Calvin cycle

A

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
Q

what is responsible for the Calvin cycle required ATP:NADPH ratio of 1.5

A

the Calvin cycle needs
9 ATPs (6 in reduction step 1, 3 in regeneration step 2)
6 NADPHs (6 in reduction step 2)

76
Q

when/why does FRET occur

A

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
Q

what makes absorption spectra different

A

unique binding sites
which AAs
more or less AAs

78
Q

how to work out the proton:NADPH of linear ET

A

6 protons are produced
C ring size = 14
3 ATPs produced
14/3 = 4.67
6/4.67 = 1.28

79
Q

PQ and PQH2 in cyclic ET

A

PQ–>PQH2

biostructures energetics and synthesis (4 decks)

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