14 - Energy conversion: Mitochondria and Chloroplasts

Question 1

Which way do the proton gradients go in mitochondria and chloroplasts?

Answer 1

Mitochondria: low [H+] in the matrix, high outside the inner membrane

chloroplasts: high inside thylakoid space (compartments within the chloroplast), high in the stroma (cross thylakoid membrane, everything here is inside the inner chloroplast membrane)

Question 2

Describe mitochondria structure

Answer 2

outer membrane, inter-membrane space, inner membrane, matrix. The inner membrane have invaginations (cristae) and more straight sections (inner boundry membrane). The junction between these is called cristae junctions.

Inner membrane is a diffusion barrier, outer membrane is permeable to small molecules. The intermembrane space therefore has the same pH as the cytoplasm, for example.

Question 3

electron affinity and redox potentials

Answer 3

NADH/NAD+ has low redox potential, are therefore good at donating electrons to stronger pairs (like O2/H2O)
transfer of an electron from NADH to O2 releases -109kj/mole, enough to synthetize ATP

this normally releases enough energy to blow up the cell, but the mitochondria splits the reactions so that the e- that is delivered to oxygen has less power.

Question 4

Mitochondria are critical for buffering the redox-potential in the cytosol - discuss/explain why

Answer 4

the shuttle system.

NADH is made in glycolosys, and glycolosys is important for the cell to live. NAD+ must be readily available for reduction. Regerenation of NAD+ from NADH happens in mitochondria, but NADH cannot cross the inner membrane. a shuttle system where smaller molecules carry the electrons from NADH (now oxidized back to NAD+) from the cytosolic side and across the inner membrane to the matrix to deliver to waiting NAD+ molecules has evolved. this allows regeneration og NAD+ in the cytosol while the mitochondria gets more NADH, facilitated by the smaller electron carriers.

Question 5

electron carriers in the electron transport chain:

Answer 5

heme group in cytochrome c
iron-sulfur clusters
ubiquinone

Question 6

electron carriers in the electron transport chain:

Answer 6

heme group in cytochrome c
iron-sulfur clusters
ubiquinone

Question 7

electron flow in electron transport chain:

Answer 7

NADH-> NADH dehydrogenase -> ubiquinone -> cytochrome c reductase -> cytochrome c -> cytochrome c oxidase -> O2

Question 8

proton pumps in the electron transport chain

Answer 8

NADH dehydrogenase, cytochrome c reductase, cytochrome c oxidase

Question 9

what cofactors are important?

Answer 9

transition metals like copper, nickel, iron, maganese

Question 10

NADH dehydrogenase

Answer 10

NADH donates 2e- to Flavin mononucleotide

As e- pass across the electron carriers,
comformational changes are transmitted along the
complex, resulting in the translocation of protons out
of the matrix.

Question 11

cytochrome c reductase

Answer 11

ubiquinone (reduced form is ubiquinol) transfers 2 e- from NADH dehydrogenase to the cytochrome c reducase. During this process, 2 H+ are pumped from the matrix to the intermembrane space.

After delivering the 2e-, ubiquinone returns to NADH dehydrogenase to collect more electrons

Question 12

cytochrome c oxidase

Answer 12

cytochrome c has the oxygen that will accept electrons inside it, bound tightly to a heme group and a copper ion. O2 is bound here to prevent formation of O2*- (O2 ion radical), which is extremely reactive and dangerous. 4 protons and 4 electrons enter one by one and make the O2 into 2H2O. This process allows another 4 H+ to be pumped out of the matrix

Question 13

supercomplex

Answer 13

The respiratory chain complexes go together to make a supercomplex to increase the efficiency of the electron transport. This also helps to increase the density of
complexes and thus the proton motive force
across the membrane

Question 14

How do the protons move out of the matrix?

Answer 14

H+ can move between water molecules due to charge, but how can they cross a hydrophobic membrane? Proton wires are rows of polar or ionic side chains in proton-translocating proteins which allow the protons to jump along the channel. Protons can move through such channels 40 times more rapidly than through bulk of water.

Question 15

ATP synthase

Answer 15

aka F-type to distinguish from other proteins capable of hydrolysing ATP

can both make and use ATP (both directions)

ATP synthase is composed of a rotor and a stator. A stalk at the periphery of the complex binds to the catalytic head to prevent it from rotating, and connects the head to stator subunits embedded in the membrane. A second stalk is connected to a rotor ring in the membrane that turns as protons flow through it. Proton flow thus makes the rotor stalk rotate inside the stationary head that connects the catalytic sites that assembles ATP. As the rotation happens, the rotor stalk changes conformation of the catalytic sites. One of the possible conformations has a high affinity for ADP + Pi, another has a higher affinity for ATP.

Question 16

Two categories of reactions happens during energy production in chloroplasts:

Answer 16

1. photosynthetic electron transfer reactions. This happens in the reaction centers in the thylakoid membrane, when a chlorophyll is excited by a photon and the electron moves along an electron-transport chain through a second reaction center. During this process, protons are pumpes across the thylakoid membrane and the resulting proton gradient is used for ATP synthesis in stroma. The final step is combinind electrons and protons with NADP+ to make NADPH. The positively charged chlorophyll that was excited is quickly stabilized by electrons from water, creating O2 gas as a by-product.
2. Carbon-fixation reactions. These don’t require light, and actually use the energy created in (1) to make sugars from CO2 using energy from ATP and reducing power from NADPH.
   CO2 combines with ribulose 1,5-bisphosphate to make 2 molecules of 3-phosphoglycerate (RUBISCO HELPS), which is processed in the Calvin cycle to glyceraldehyde 3-phosphate (midway through cycle). 1/6 of the glyceraldehyde 3-phosphates leave the cycle to make sugars, fats, AAs, while the others continue to make more ribulose 1,5 bisphosphate to fixate more CO2.

Question 17

What happens when a chlorophyll is excited?

Answer 17

The electron is returned to the ground state in one of three ways:

1. By converting the extra energy into heat (molecular motion) or to some combination of heat and light of a longer wavelengths (fluorescence), which is what usually happens to isolated chlorophylls in solution
2. By transferring the energy - but not the electron - directly to a neighboring chlorophyll molecule by a process called resonance energy transfer
3. By transferring the excited electron with its negative charge to another nearby molecule, an electron acceptor, after which the positively charged chlorophyll returns to its original state by taking up an electron from some other molecule, an electron donor.

When excited by a photon, most chlorophylls simply transmit the absorbed energy to another nearby chlorophyll by resonance energy transfer. In some specifically positioned chlorophylls (special pairs), the energy difference between the ground and excited state is just right for the photon to trigger a light-induced chemical reaction. The photosynthetic electron transfer process happens when a chlorophyll in a special pair ionizes. The electron is passed to a quinone (electron carrier, can give the e- to the electron transport chain) in the same protein complex, preventing it from reassociating with the positive chlorophyll ion and ensuring charge separation. The chlorophyll is a very strong oxidant and is able to withdraw an electron from another substrate (water).

Question 18

Two types of chloropyll-protein complexes exist:

Answer 18

antenna complexes collect the energy from many electrons
reaction centers are the place for charge separation

together these two make up a photosystem

Question 19

What happens to the protons from the water that loses its electron to stabilize an ionized chlorophyll?

Answer 19

the protons add to the proton gradient, the O2 is released

Question 20

Z scheme

Answer 20

The electron movement (and energy) looks like a sideway Z.

Electron is excited and captured by the electron carrier plastoquinone (ensuring charge separation) in PSII. e- passes through cytochrome b6-f complex (protons are pumped). Another electron carrier, plastocyanine, receives the e- and carries it to PSI. PSI receives electrons from plastocyanin in the thylakoid space and transfers them, via a second charge-separation reaction, to the small protein ferredoxin on the
opposite membrane surface. Then, in a final step, ferredoxin feeds its electrons to a membrane-associated enzyme complex, the ferredoxin-NADP+ reductase, which uses the electrons to produce NADPH from NADP+

ATP is formed using the proton gradient generated by the light reactions.

The Z scheme is necessary to bridge the very large energy gap between water and NADPH. A single quantum of visible light does not contain enough energy to excite two electrons from water, especially as water is a poor electron donor and NADP+ is a poor acceptor. Other species that only have one PS use more high-energy compounds than water as electron donor.

Question 21

How can PSII steal an e- from water?

Answer 21

water is plentiful, but difficult to extract an e- from. PSII has a manganese cluster linked to the protein, The reaction 2H2O + 4 photons -> 2H+ + 4 e- + O2 is catalyzed by the manganese cluster, and the intermediates remain firmly attached to the manganese cluster until two molecules of water have been fully oxidized to O2, thus ensuring that no dangerous O2 radicals are released. The protons are released into the thylakoid space to contribute to the proton gradient.

Question 22

What makes it so the plant can switch between making more ATP or NADPH?

Answer 22

Starting with the withdrawal of electrons from water, the light-driven charge-separation steps in PSII and I enable the energetically unfavorable flow of electrons from water to NADPH. Three small mobile electron carriers - plastoquinone, plastocyanin, and ferredoxin - participate in this process. Together with the electron-driven proton pump of the cytochrome b6-f complex, the PSs generate a large proton gradient across the thylakoid membrane. The ATP synthase molecules embedded in the thylakoid membranes then harness this proton gradient to produce ATP in stroma.
The linear Z scheme for photosynthesis thus far discussed can switch to a circular mode of electron flow through PSI and the b6-f complex to reduce plastoquinone, instead of passing its electrons to the ferredoxin-NADP+ reductase enzyme complex. This turns PSI into a light-driven proton pump, thereby increasing the proton gradient and the amount of ATP made. Depending on whether the plant needs more ATP (circular) or NADPH (linear), the cell can switch between these two modes.