Enzyme binding environments

[esob]

I'm a little confused on binding sites in general, since we never went into that much detail in elementary biochem. I have watched all the KA videos and done the EK review but am still a bit hazy.

Do hydrophobic binding sites on enzymes mean that they will interact preferably with hydrophobic amino acids? What about with hydrophilic AA's?

For example, if given the binding site of 3 enzymes A,B and C, where:

The binding site of enzyme A is Glutamic acid
The binding site of enzyme B is Valine
The binding site of enzyme C is Lysine


Which enzyme would prefer to interact with an Arg/ Ala/Asp/ residue from the substrate and what is the method of reasoning behind it? Normally I think that pos charged AA's prefer to interact w/ neg charged AA's but this doesn't always seem to be the case when dealing with enzymes and their substrates.

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[CommyO]

I'm a little confused on binding sites in general, since we never went into that much detail in elementary biochem. I have watched all the KA videos and done the EK review but am still a bit hazy.

Do hydrophobic binding sites on enzymes mean that they will interact preferably with hydrophobic amino acids? What about with hydrophilic AA's?

For example, if given the binding site of 3 enzymes A,B and C, where:

The binding site of enzyme A is Glutamic acid
The binding site of enzyme B is Valine
The binding site of enzyme C is Lysine


Which enzyme would prefer to interact with an Arg/ Ala/Asp/ residue from the substrate and what is the method of reasoning behind it? Normally I think that pos charged AA's prefer to interact w/ neg charged AA's but this doesn't always seem to be the case when dealing with enzymes and their substrates.

You're right in your reasoning in that positively charged binding sites which contain H, K, R would bind negatively charged AAs such as D and E (Trypsin). Can you give me a case that is the exception?

Hydrophobic sites are a bit more interesting. A small nonpolar amino acid would normally be found in binding sites that attract aromatic substrates such as chymotrypsin or any substrates with W, F, Y AAs. Larger AAs in binding site will promote binding of substrates with smaller nonpolar AAs

A hydrophilic AA containing substrate will not bind to an enzyme with hydrophobic AA

 

[esob]

You're right in your reasoning in that positively charged binding sites which contain H, K, R would bind negatively charged AAs such as D and E (Trypsin). Can you give me a case that is the exception?

Hydrophobic sites are a bit more interesting. A small nonpolar amino acid would normally be found in binding sites that attract aromatic substrates such as chymotrypsin or any substrates with W, F, Y AAs. Larger AAs in binding site will promote binding of substrates with smaller nonpolar AAs

A hydrophilic AA containing substrate will not bind to an enzyme with hydrophobic AA

Thanks, I'll have to look back through the SB, but there was one question that seemed to state the correct answer was a hydrophobic AA in the binding site next to another hydrophobic AA b/c it would "stabilize" the binding site. At this point, all the questions are starting to run together though, lol.