Slide 1

1a) Top (extracellular to intracellular)11a) Side

extracellularintracellularInside cell membrane2

1a) Bottom (intracellular to extracellular)31a) At the top of the protein, there are basic and acidic residues. The acidic residues are located in the center of the protein around the channel. The basic residues are on the outside ring of the protein. These form the ring on the outside of the protein that help hold the shape of the pore. The bottom of the protein has basic and acidic residues as well. The acidic residues surround the pore whereas the basic residues form an outer ring around the pore. These basic residues help hold the pore open and anchor the acidic residues in place.

1b5

1d)1b) Inside the protein, its easier to see the separation of where the acidic and basic residues of the protein are located. At the top of the protein, there are red, acidic residues and at the bottom of the protein, there are blue, basic residues . These polar residues are concentrated at the parts of the protein that are exposed to the polar solvents in the intracellular and extracellular membrane.

1c) There are 3 potassiums bound to the protein. They are held in place by ionic dipole interactions. The proteins are all positively charged ions. They are held to the protein by the slightly charged residues of the amino acids surrounding the protein. The acidic residues help hold the potassium ions.

1d) This protein is a transmembrane protein, it passes through the membrane and connects the intracellular space with extracellular space. A part of it is enclosed between the lipid bilayers which means the residues have to be non-polar. The middle part of the protein shows nearly all yellow, non-polar residues, proving this. The parts of the protein in the extracellular and intracellular spaces have acidic and basic residues, allowing them to be in the polar solvent, water, that is present in the extracellular and intracellular spaces. The polar residues also help the potassium ions to move through the channel; one end attracts the ions into the proteins and the polar residues on the other end pulls it through the protein across the membrane.

1e) The interior of the protein is non-polar, so the polar parts of amino acids face to the pore. The non polar carbons on the amino acids interact with the inside of the cell. The polar residues help move the potassium ion through the protein. The nonpolar parts of the protein interacting with the rest of the molecules hold the pore open in place and allow it to remain in place. 2)

92) The channel is able to distinguish between the K+ and the Na+ because of the differences in size of the ion. The K+ is a larger ion than the Na+. When in an aqueous solution, these ions get hydrated, surrounded by water molecules. Since the K+ is a larger ion, there is a larger distance between the K+ and the water molecules surrounding it. The bond between them is pretty weak compared to the bond between the Na+ and water. The Na+ has a much smaller ion radius than the K+ and so the distance between its nucleus and the water molecules is much smaller, therefore, making the bond stronger. It is more stable and energetically favorable for the Na+ to be hydrated. When these hydrated molecules come to the channel, the K+ can easily slip in because of the weak ion-dipole interactions between the K+ and the water. It is easier to dehydrate the K+ and to replace the water with a carboxy group from the carbonyl. For Na+, it is different, it requires a large amount of energy to dehydrate the water molecules and the Na+ surrounded by water molecules is too big to fit through the channel, therefore it is repelled. Even though the carbonyl group uses the same amount of energy to interact with the K+ and the Na+ since its distance doesnt change, it is almost impossible for the Na+ to get into the channel to react with the carbonyl. The water molecules are held very tightly to the Na+ ion and take too much energy to remove it.

3)

3a)

H-bondVan-der-Waals

123) Around the pore are a series of aromatic rings that form a very specific shape. The main protein residues at play are Tyrosine, Tyr and Tryptophan, Trp. The Tyr are at the center of this network of rings. Its carbonyl group lines the center of the pore and its OH group serves to hold it in place. The OH groups of the Tyr form H bonds with the N of the neighboring Trp. They form a very solid, and strong network of H-bonds that serve to hold the pore open, and the amino acids in shape. The pore is also held open by Van der Waals interactions between the non-polar carbons of Trp and Tyr.