Alice Rhee Feb.

24th 2011 – week 8

Email: Hrhee@ucsd.edu
AIM: AliceHRhee
Website: Bibc100wi11.tumblr.com (password protected)

K+ Channel continued
What goes down in the selectivity filter of K+ channel?
- Ion pore made between the four monomers.
- Each monomer is made of 2 transmembrane α-helices, 1 pore helix and a cytosolic tail.
- Hole in the centerwhich forms the ion pore through the membrane helix
- C term TM helix faces the central pore while the N term helix faces the lipid membrane
- Pore helices form selectivity loop – selectivity filter
- Selectivity loop – various carbonyl oxygens
- Carbonyl oxygen accommodate the K+ “surrogate” water molecules
- Main-chain atoms create a stack of sequential oxygen rings along the passage to bind to
dehydrated K+ ions
- Ion enters with a hydration shell enters the selectivity filter it dehydrates. Binding to the
carbonyl oxygen atoms in the filter compensates the energetic cost of dehydration
- Dimensions of the binding sites are such that K+ ion fits in the filter precisely so that the
energetic costs and gains are well balanced.

- Sodium is smaller than potassium ion and it is very similar in shape and charge. How could
potassium channel only pass K+? Shouldn’t it be easier to pass a smaller ion?

 The key is Desolvation energy.

-8 water molecules are needed to stabilize K+ whereas 6 is necessary for stabilizing a Sodium ion,
which is SMALLER.

- In the figure to the left, going

from (A) to (B) requires
desolvation energy
- You can tell that the two states for
potassium ion exist somewhat
close to equilibrium. However, the
RESOLVED state (A) is favored
for the Sodium ion.
- Also, you can think of it in terms
of distance. Even though the
sodium is smaller than potassium,
the distance between the ion and
the carbonyl is LARGER for the
sodium. Thus, it is more difficult to stabilize sodium in the filter of carbonyls.

More explanations:
- For Potassium, the desolvation energy (energy required to remove water around the ion) is similar to
resolvation of the ion in the K+ channel. In other words, stabilizing the K+ ion in the filter is easier
because it’s quite like stabilizing it with water molecules in the hydrophilic environment.
- For Sodium, the resolvation Energy is MUCH less than desolvation energy.

 Potassium ions get ‘pushed’ down the gradient

- When two potassium ions enter the filter, electrostatic forces them apart. Thus as a K+ enters the
filter, the next ion coming in will push the first ion to the other side. (positively charged ions repel
one another)
o It’s like sweaty people at Sungod pushing other people to the front of the stage. Sweat –
repulsive force. (Please don’t use my analogies on a test – I appreciate it but only do it if
you have extra time i.e. after you seriously answer the questions)

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 Alice Rhee Feb. 24th 2011 – week 8
Email: Hrhee@ucsd.edu
AIM: AliceHRhee
Website: Bibc100wi11.tumblr.com (password protected)

Bacterial Photosynthetic Reaction Center

- Built up from four different polypeptide chains and many
QuickTimeª and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
pigments
- Protein complex was a photosynthetic reaction center from
the photosynthetic purple bacterium Rhodopseudomonas ciridis-
converts the energy of captured sunlight into electrical and
chemical energy in the first steps oh photosynthesis by pumping
protons from one side of a membrane to another.
- Photosynthetic reaction centers are embedded in the
membrane of the vesicles

- Reaction center is built from four polypeptide chains – three

of which are called L, M, and H
- H is the heaviest, L is lightest
- Reaction center contains pigments
- L and M subunits are firmly anchored in the membrane each
by five hydrophobic transmembrane alpha helices
- L and M are structurally similar
- H subunit has one transmembrane alpha helix
- Alpha helices D and E from the L and M subunits form the core of the membrane-spanning part of the
complex.
* The fourth subunit of the reaction center is a cytochrome that has 336 amino acids. This cytochrome is
unique in structure – different than cytochromes not found in bacteriorhodopsin. The C subunit is a four-
heme containing c-type cytochrome. Cytochrome is an electron DONOR.

 Core of the membrane spanning part of the comoplex:

Alpha helices D and E (from L and H subunit. L and H each has D and E helices as noted in the
colored picture on top of this page)
These four alpha helices (D and E from L subunit and D and E from H subunit) are tightly packed.
Each of these helices has a histidine side chain as ligand to the Fe atom, which is located between
the helices close to the cytoplasm.
Role of Fe is to stabilize the structure of the four helix bundle DOES NOT have a functional role
in electron transfer

 Photosynthetic Pigments:
The reaction center contains PIGMENTS. These are used to
capture photons and for electron flow from one side of a membrane
to the other side. They are bound to the L and M subunits.

1) The special pair of chlorophyll molecules – initiates electron

transfer across the membrane.
2) Accessory chlorophylls (bacteriochlorophyll) – contains Mg
in the center.
3) Pheophytin
4) Qb and Qa (Quinone) – Qb is the electron accepter at the
END. Qb transfers a proton to the outside of the membrane
(creating a proton gradient).
a. Cytochrome subunit accepts the electron from Qb
and excites the special pair of chloryphylls to
repeat the entire process.

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Alice Rhee Feb. 24th 2011 – week 8
Email: Hrhee@ucsd.edu
AIM: AliceHRhee
Website: Bibc100wi11.tumblr.com (password protected)

Light Harvesting Complexes

- Chlorophyll molecules of the reaction center cannot be the only photon
accepter in the bacterial membrane there must be a light-harvesting complex

2 LH2 ‘s

RXN LH1
center

LH2 structure
- alpha (light blue) and beta (green) helices. Both helices are
transmembrane alpha helices. Each has histidine residues sticking
out to stabilize the bacteriochlorophyll molecule (dark blue /
purple lines) by binding to the Mg molecule in the center.
- 9 alpha / 9 beta / 18 bacteriochlorophylls
Transmembrane alpha helices –
- To span the lipid bilayer a minimum of about 20 amino acids are
required
- Photosynthetic reaction center these alpha helices each comprise
about 25-30 residues