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CHE 541 > 8 - Bacteriorhodopsin > Flashcards

8 - Bacteriorhodopsin Flashcards

1
Q

What does bacteriorhodopsin do?

A

It uses light to pump protons across the membrane

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2
Q

Which amino acid is important for the proton gradient?

A

Asp - unprot in hydrophilic, prot at edge (more hydrophobic)

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3
Q

How is the proton gradient established in mitochrondria?

A

Through cytochrome proteins

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4
Q

What was the controversy about ATP synthase in the 1960s?

A

People thought it worked due to conformational change, but it actually works through proton gradient

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5
Q

What experiment showed that ATP synthase used a proton gradient?

A
  1. ATP synthase and bacteriorhodopsin were constituted in lipid vesicles
  2. Added ADP and light, and saw ATP being produced
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6
Q

What bacteria is bacteriorhodopsin from?

A

Haloarchaea

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7
Q

Where do haloarchaea live?

A

In salt flats

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8
Q

Why do haloarchaea have a purple color?

A

From the retinal (absorb light)

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9
Q

What is another name for retinal?

A

Vitamin A

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10
Q

How long is the cycle from trans to cis in retinal?

A

~1 ms

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11
Q

What happens when retinal absorbs light?

A

It goes from trans to cis

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12
Q

What is attached to the retinal?

A

Lys

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13
Q

What happens to the Schiff base during the reaction?

A

It gets deprotonated (pumped across membrane)

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14
Q

What was the first retinal binding protein discovered?

A

Rhodopsin in the eye

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15
Q

What is optogenetics?

A

Use light to open ion channels on neurons

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16
Q

What are some other members of the bacteriorhodopsin family?

A

Chloride pumps (halorhodopsin), phototaxis (sensory rhodopsins), ion channels (channel rhodopsins), and marine bacteria proton pump (proterorhodopsin)

17
Q

What is the structure of bacterorhodopsin?

A

7 transmembrane helices, retinal in middle

18
Q

What are the steps of the bacteriorhodopsin pathway?

A
  1. Use light to isomerize to retinal 13-cis (K/L)
  2. Protonate equilibrium between Schiff base and Asp85 (M1)
  3. Switch and release proton to outside (M2/M2’)
  4. Reprotonation of Schiff base by Asp96 (N)
  5. Reprotonation of Asp96, reisomerization of retinal to all trans (O)
  6. Deprotonation of Asp85 (back to bR)
19
Q

What direction does the retinal move when it isomerizes?

A

Away from the direction it pumps

20
Q

Where is Asp212 located and what does it do?

A

Located next to Asp85, and helps stabilize protonated Schiff base

21
Q

True or false: bR has functional water

A

True: they aid in H-bonding, which is important for the intermediates

22
Q

What happens when the retinal isomerizes?

A

The Schiff base is put into a hydrophobic environment, dropping the pKa (want to deprot)

23
Q

How does the Schiff base in bR get deprot?

A

The Asp85 (deprot) is not stabilized, so its pKa changes and it gets prot

24
Q

What is the energy of a photon?

A

50 kcal/mol

25
Q

What happens when Asp85 gets prot?

A

Arg82 (prot) is not stabilized by negative charge, so it swings over to Glu194-Glu204 pair

26
Q

What is the Glu-Glu pair similar to?

A

Asp proteases

27
Q

What are the initial states of the Glu-Glu pair?

A

One prot, one unprot

28
Q

What happens when Arg82 interacts with the Glu-Glu pair?

A

Glu204 deprot (pKa drops, stabilized by new positive charge on Arg82)

29
Q

What happens to TM6 when Asp85 gets prot?

A

It moves, allowing water to interact with Asp96

30
Q

How does TM6 get moved?

A

Methyl group pushes on Trp182, acts as a lever to push helix

31
Q

How is prot Arg82 stabilized in br?

A

Through water molecules

32
Q

What is unique about Arg partial positive charge?

A

It is distributed over many atoms

33
Q

What happens when Asp96 is exposed to water?

A

The pKa of Asp96 (prot) drops (stabilized by H-bonds), thus reprot the Schiff base

34
Q

What happens when the Schiff base is reprot?

A

It triggers the thermal reisomerization to all trans

35
Q

What happens when retinal reisomerizes?

A
  1. TM6 moves back to close cavity and force water back out, which reprot Asp96 by picking up a proton from the cell
  2. Asp85 deprot (due to prot Schiff base), Glu204 reprot, and Arg82 swings back to Asp85
36
Q

What is the general overview of the bR reaction?

A

Series of protonation changes, directed by pKa modulations and small movements in the protein

37
Q

How can bR be turned into a Cl- pump?

A

By mutating Asp85 to Thr85

38
Q

How does Thr85 interact with the mutated bR?

A

It is neutral, and chloride can enter

39
Q

How does the mutated bR work?

A

When retinal reisomerizes, the Cl- follows NH+ on Schiff base, and Cl- can enter cytoplasm when TM6 moves to allow water in

CHE 541 (20 decks)

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