Enzyme amino acid composition

[Necr0sis713]

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I have a question for you biochem guys out there.

I'm pretty good with AA's as of now, but I have one problem. I know that the interior of a protein in a water environment is hydrophobic, and the interior of the bilayer is hydrophobic too.

But, what would the amino acid composition be of a membrane protein on the interior? I had a question wrong asking me "What would the AA composition be of a protein channel for a sodium channel" and I chose aspartate, and I got it wrong. Why aspartate? I sort of reasoned that since sodium is positively charged, we would need a negatively charged amino acid to interact with it. The answer was simply hydrophobic amino acid because it was the interior of the membrane.

Does that logic apply to the interior of all enzymes? Or just channel protein because they're embbeded in the bilayer?

What if a regular enzyme in the cytosol interacted with an amino acid, wouldn't say a negative AA residue on the enzyme (like aspartate) need to interact with + charged substrates? Or is it strictly that the interior of ALL amino acids are hydrophobic.

 

[aldol16]

The sodium channel question is flawed because it really all depends on the nature of the channel. If a channel is funneling polar/charged substrates into/out of the cell, it must be polar and/or charged. Think about why. A polar molecule cannot diffuse across the cell membrane because the membrane is hydrophobic. So to make the process thermodynamically feasible, the protein channel provides a hydrophilic, polar channel so that the substrate can pass through. Now, on the outside of the that channel (the side facing the lipid bilayer), the residues would be hydrophobic. This can be easily observed with transmembrane beta barrels, where you can have all residues on one face of the barrel facing inward and polar and residues on the other side facing outward and nonpolar.

 

[Necr0sis713]

The sodium channel question is flawed because it really all depends on the nature of the channel. If a channel is funneling polar/charged substrates into/out of the cell, it must be polar and/or charged. Think about why. A polar molecule cannot diffuse across the cell membrane because the membrane is hydrophobic. So to make the process thermodynamically feasible, the protein channel provides a hydrophilic, polar channel so that the substrate can pass through. Now, on the outside of the that channel (the side facing the lipid bilayer), the residues would be hydrophobic. This can be easily observed with transmembrane beta barrels, where you can have all residues on one face of the barrel facing inward and polar and residues on the other side facing outward and nonpolar.

Thank you. Yeah I had a feeling that since the inside has to interact with the + charged substrates, it should have a hydrophillic interior. I do understand too that basically, whatever interacts with the inside of the bilayer has to be hydrophobic.

Maybe the question was asking about the outside of the channel? I forgot where I had it so I can't refer back to it honestly. But thank you.

 

[NextStepTutor_2]

I have a question for you biochem guys out there.

I'm pretty good with AA's as of now, but I have one problem. I know that the interior of a protein in a water environment is hydrophobic, and the interior of the bilayer is hydrophobic too.

But, what would the amino acid composition be of a membrane protein on the interior? I had a question wrong asking me "What would the AA composition be of a protein channel for a sodium channel" and I chose aspartate, and I got it wrong. Why aspartate? I sort of reasoned that since sodium is positively charged, we would need a negatively charged amino acid to interact with it. The answer was simply hydrophobic amino acid because it was the interior of the membrane.

Does that logic apply to the interior of all enzymes? Or just channel protein because they're embbeded in the bilayer?

What if a regular enzyme in the cytosol interacted with an amino acid, wouldn't say a negative AA residue on the enzyme (like aspartate) need to interact with + charged substrates? Or is it strictly that the interior of ALL amino acids are hydrophobic.

The could have asked (as the AAMC Qs and our own NextStep Full Lengths do) about a specific location on the channel (interior vs. exterior). this can be said for trans membrane proteins as well, cytosol facing vs. membrane interior.

Your thinking was spot on.

Good luck and keep studying!