1a) Top (extracellular to

intracellular)

1a) Side
extracellular

Inside cell membrane

intracellular

1a) Bottom (intracellular to

extracellular)

1a) 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.

1b

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

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)

2) 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)

Hbond

Van-der-Waals

3) 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 Hbonds 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.